Mercurial > repos > galaxyp > openms_mapalignerspectrum
changeset 8:085863ba8f0e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:24:40 +0000 |
| parents | 401a83dcff39 |
| children | c4c64002d01e |
| files | 404-urls.patch MapAlignerSpectrum.xml OMSSAAdapter.patch PepNovoAdapter.patch filetypes.txt fill_ctd.py fill_ctd_clargs.py generate-foo.sh generate.sh hardcoded_params.json macros.xml macros_autotest.xml macros_discarded_auto.xml macros_test.xml prepare_test_data_manual.sh readme.md test-data.sh test-data/pepnovo_models.loc test-data/random.fa test-data/random_RNA.fa tools_blacklist.txt |
| diffstat | 21 files changed, 365 insertions(+), 28822 deletions(-) [+] |
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--- a/404-urls.patch Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml ---- FeatureFinderSuperHirn.xml 2020-10-02 12:06:56.398572301 +0200 -+++ FeatureFinderSuperHirn.xml 2020-10-02 12:07:31.511153834 +0200 -@@ -105,6 +105,6 @@ - <help><![CDATA[Finds mass spectrometric features in mass spectra. - - --For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help> -+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help> - <expand macro="references"/> - </tool>
--- a/MapAlignerSpectrum.xml Fri Nov 06 19:46:06 2020 +0000 +++ b/MapAlignerSpectrum.xml Thu Dec 01 19:24:40 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Map Alignment]--> -<tool id="MapAlignerSpectrum" name="MapAlignerSpectrum" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MapAlignerSpectrum" name="MapAlignerSpectrum" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Corrects retention time distortions between maps by spectrum alignment.</description> <macros> <token name="@EXECUTABLE@">MapAlignerSpectrum</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -16,13 +14,20 @@ #import re ## Preprocessing -mkdir in && -${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir in_cond.in && +#if $in_cond.in_select == "no" +mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && +${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +#end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && + mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && #end if #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir trafo_out && + mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && #end if ## Main program call @@ -32,14 +37,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in -${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +#if $in_cond.in_select == "no" +${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' +#end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out - ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("mzml")) for _ in $in if _])} + ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("mzml")) for i, f in enumerate($in_cond.in) if f])} #end if #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -trafo_out - ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} + ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])} #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' @@ -47,10 +56,10 @@ ## Postprocessing #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') - ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("mzml")} for _ in $out if _])} + ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("mzml")} for i, f in enumerate($in_cond.in) if f])} #end if #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') - ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])} + ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])} #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' @@ -60,45 +69,54 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/> + <conditional name="in_cond"> + <param name="in_select" type="select" label="Run tool in batch mode for -in"> + <option value="no">No: process all datasets jointly</option> + <option value="yes">Yes: process each dataset in an independent job</option> + </param> + <when value="no"> + <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/> + </when> + </conditional> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> <param name="gapcost" argument="-algorithm:gapcost" type="float" optional="true" min="0.0" value="1.0" label="This Parameter stands for the cost of opening a gap in the Alignment" help="A gap means that one spectrum can not be aligned directly to another spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagine it as a insert or delete of the spectrum in the map (similar to sequence alignment). The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and needs to carry a punishment, so a gap should only be opened if the benefits outweigh the downsides. The Parameter is to giving as a positive number, the implementation convert it to a negative number"/> - <param name="affinegapcost" argument="-algorithm:affinegapcost" type="float" optional="true" min="0.0" value="0.5" label="This Parameter controls the cost of extension a already open gap" help="The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure of gaps interspersed with matches (gap match gap match etc.). Therefor the punishment for the extension of a gap generally should be lower than the normal gapcost. If the result of the alignment shows high compression, it is a good idea to lower either the affine gapcost or gap opening cost"/> + <param name="affinegapcost" argument="-algorithm:affinegapcost" type="float" optional="true" min="0.0" value="0.5" label="This Parameter controls the cost of extension a already open gap" help="The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure of gaps interspersed with matches (gap match gap match etc.). Therefore the punishment for the extension of a gap generally should be lower than the normal gapcost. If the result of the alignment shows high compression, it is a good idea to lower either the affine gapcost or gap opening cost"/> <param name="cutoff_score" argument="-algorithm:cutoff_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="The Parameter defines the threshold which filtered spectra, these spectra are high potential candidate for deciding the interval of a sub-alignment" help="Only those pair of spectra are selected, which has a score higher or same of the threshold"/> <param name="bucketsize" argument="-algorithm:bucketsize" type="integer" optional="true" min="1" value="100" label="Defines the numbers of buckets" help="It is a quantize of the interval of those points, which defines the main alignment (match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve"/> <param name="anchorpoints" argument="-algorithm:anchorpoints" type="integer" optional="true" min="1" max="100" value="100" label="Defines the percent of numbers of match points which a selected from one bucket" help="The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve"/> <param name="mismatchscore" argument="-algorithm:mismatchscore" type="float" optional="true" max="0.0" value="-5.0" label="Defines the score of two spectra if they have no similarity to each othe" help=""/> - <param name="scorefunction" argument="-algorithm:scorefunction" display="radio" type="select" optional="false" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available"> + <param name="scorefunction" argument="-algorithm:scorefunction" type="select" optional="true" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available"> <option value="SteinScottImproveScore" selected="true">SteinScottImproveScore</option> <option value="ZhangSimilarityScore">ZhangSimilarityScore</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="scorefunction"/> </param> </section> <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> - <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help=""> + <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help=""> <option value="linear">linear</option> <option value="b_spline">b_spline</option> <option value="lowess">lowess</option> <option value="interpolated" selected="true">interpolated</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="type"/> </param> <section name="linear" title="Parameters for 'linear' model" help="" expanded="false"> <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/> - <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help=""> - <option value="">default (nothing chosen)</option> + <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help=""> <option value="1/x">1/x</option> <option value="1/x2">1/x2</option> <option value="ln(x)">ln(x)</option> <option value=""></option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="x_weight"/> </param> - <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help=""> - <option value="">default (nothing chosen)</option> + <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help=""> <option value="1/y">1/y</option> <option value="1/y2">1/y2</option> <option value="ln(y)">ln(y)</option> <option value=""></option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="y_weight"/> </param> <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/> <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/> @@ -108,12 +126,12 @@ <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false"> <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/> <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/> - <param name="extrapolate" argument="-model:b_spline:extrapolate" display="radio" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)"> + <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)"> <option value="linear" selected="true">linear</option> <option value="b_spline">b_spline</option> <option value="constant">constant</option> <option value="global_linear">global_linear</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="extrapolate"/> </param> <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/> </section> @@ -121,38 +139,38 @@ <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/> <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/> <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/> - <param name="interpolation_type" argument="-model:lowess:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation"> + <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation"> <option value="linear">linear</option> <option value="cspline" selected="true">cspline</option> <option value="akima">akima</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="interpolation_type"/> </param> - <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation"> + <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation"> <option value="two-point-linear">two-point-linear</option> <option value="four-point-linear" selected="true">four-point-linear</option> <option value="global-linear">global-linear</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="extrapolation_type"/> </param> </section> <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false"> - <param name="interpolation_type" argument="-model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help=""> + <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help=""> <option value="linear">linear</option> <option value="cspline" selected="true">cspline</option> <option value="akima">akima</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="interpolation_type"/> </param> - <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" display="radio" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border"> + <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border"> <option value="two-point-linear" selected="true">two-point-linear</option> <option value="four-point-linear">four-point-linear</option> <option value="global-linear">global-linear</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="extrapolation_type"/> </param> </section> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -163,11 +181,11 @@ </inputs> <outputs> <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> - <discover_datasets directory="out" format="mzml" pattern="__name__"/> + <discover_datasets directory="out" recurse="true" format="mzml" pattern="__name__"/> <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> </collection> <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out"> - <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/> + <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/> <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> </collection> <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> @@ -177,13 +195,65 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MapAlignerSpectrum"/> - <expand macro="manutest_MapAlignerSpectrum"/> + <tests><!-- TOPP_MapAlignerSpectrum_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> + </conditional> + <output_collection name="out" count="3"/> + <section name="algorithm"> + <param name="gapcost" value="1.0"/> + <param name="affinegapcost" value="0.5"/> + <param name="cutoff_score" value="0.7"/> + <param name="bucketsize" value="100"/> + <param name="anchorpoints" value="100"/> + <param name="mismatchscore" value="-5.0"/> + <param name="scorefunction" value="SteinScottImproveScore"/> + </section> + <section name="model"> + <param name="type" value="interpolated"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight"/> + <param name="y_weight"/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Corrects retention time distortions between maps by spectrum alignment. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerSpectrum.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerSpectrum.html]]></help> <expand macro="references"/> </tool>
--- a/OMSSAAdapter.patch Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ ---- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200 -+++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200 -@@ -22,6 +22,7 @@ - mkdir database && - ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - -+makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - ## Main program call - - set -o pipefail &&
--- a/PepNovoAdapter.patch Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ ---- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 -+++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 -@@ -42,8 +42,13 @@ - </configfiles> - <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> -- <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> -- <expand macro="list_string_san"/> -+ <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="0"/> -+ <column name="value" index="2"/> -+ <filter type="unique_value" name="unique_set" column="0"/> -+ <validator type="no_options" message="No model directory available"/> -+ </options> - </param> - <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> - <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> -@@ -51,8 +56,14 @@ - <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> - <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> - <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> -- <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> -- <expand macro="list_string_san"/> -+ <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="1"/> -+ <column name="value" index="1"/> -+ <filter type="param_value" ref="model_directory" column="2"/> -+ <filter type="unique_value" column="1"/> -+ <validator type="no_options" message="No model available"/> -+ </options> - </param> - <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> - <option value="TRYPSIN" selected="true">TRYPSIN</option>
--- a/filetypes.txt Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -# CTD type # Galaxy type -# the following lines need to be at the top in order to ensure -# correct translation Galaxy->CTD type for the ambiguous cases -# (should only be relevant for the autogenerated tests [which -# do not set the ftype of the inputs]) -txt txt -tsv tabular - -##analysisXML -# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters -bioml xml -consensusXML consensusxml -# TODO csv is problematic, since csv often actually means tsv .. but not always -csv csv -##dat -dta dta -dta2d dta2d -edta edta -fa fasta -fas fasta -fasta fasta -FASTA fasta -featureXML featurexml -featurexml featurexml -# fid -html html -HTML html -idXML idxml -##ini txt -json json -kroenik kroenik -mascotXML mascotxml -mgf mgf -mrm mrm -ms sirius.ms -ms2 ms2 -msp msp -mzData mzdata -mzid mzid -# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444 -mzML mzml -mzml mzml -mzq mzq -mzTab mztab -mzXML mzxml -novor txt -obo obo -# I guess this is the idXML output of omssa -omssaXML idxml -osw osw -OSW osw -params txt -paramXML paramxml -fasta peff -peplist peplist -# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests -pep.xml pepxml -pepXML pepxml -png png -PNG png -protXML protxml -psms psms -# TODO implement or use -# psq -pqp pqp -qcML qcml -spec.xml spec.xml -splib splib -sqMass sqmass -tandem.xml tandem -trafoXML trafoxml -traML traml -TraML traml -tab tabular -## MOVED TO TOP txt txt -raw thermo.raw -## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419 -xls tsv -XML xml -xml xml -xquest.xml xquest.xml -xsd xml - -# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml -# cachedMzML xml
--- a/fill_ctd.py Fri Nov 06 19:46:06 2020 +0000 +++ b/fill_ctd.py Thu Dec 01 19:24:40 2022 +0000 @@ -32,7 +32,7 @@ for k, v in e.items(): if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): mergeDicts(d[k], e[k]) - elif k not in d and not isinstance(e[k], collections.abc.Mapping): + elif k not in d: d[k] = e[k] else: sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) @@ -135,9 +135,10 @@ # insert the hc_args into the args mergeDicts(args, hc_args) -if "adv_opts_cond" in args: - args.update(args["adv_opts_cond"]) - del args["adv_opts_cond"] +# put the contents of the advanced options section into the main dict +if "adv_opts" in args: + args.update(args["adv_opts"]) + del args["adv_opts"] # IDMapper has in and spectra:in params, in is used in out as format_source", # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
--- a/fill_ctd_clargs.py Fri Nov 06 19:46:06 2020 +0000 +++ b/fill_ctd_clargs.py Thu Dec 01 19:24:40 2022 +0000 @@ -1,40 +1,70 @@ #!/usr/bin/env python3 + +import operator from argparse import ArgumentParser +from functools import reduce # forward compatibility for Python 3 from io import StringIO from CTDopts.CTDopts import ( + _Null, CTDModel, ModelTypeError, Parameters ) + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + if __name__ == "__main__": # note add_help=False since otherwise arguments starting with -h will # trigger an error (despite allow_abbreviate) parser = ArgumentParser(prog="fill_ctd_clargs", description="fill command line arguments" - "into a CTD file and write the CTD file to", + "into a CTD file and write the CTD file to stdout", add_help=False, allow_abbrev=False) - parser.add_argument("--ctd", dest="ctd", help="input ctd file", - metavar='CTD', default=None, required=True) + parser.add_argument("--ini_file", dest="ini_file", help="input ini file", + metavar='INI', default=None, required=True) + parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" + "if given then optional parameters from the ini file" + "will be filled with the defaults from this CTD file", + metavar='CTD', default=None, required=False) args, cliargs = parser.parse_known_args() + # load CTDModel - model = None + ini_model = None try: - model = CTDModel(from_file=args.ctd) + ini_model = CTDModel(from_file=args.ini_file) except ModelTypeError: pass try: - model = Parameters(from_file=args.ctd) + ini_model = Parameters(from_file=args.ini_file) except ModelTypeError: pass - assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) # get a dictionary of the ctd arguments where the values of the parameters # given on the command line are overwritten - margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) + ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) + + if args.ctd_file: + ctd_model = CTDModel(from_file=args.ctd_file) + ctd_values = ctd_model.get_defaults() + for param in ini_model.get_parameters(): + if not param.required and (param.default is None or type(param.default) is _Null): + lineage = param.get_lineage(name_only=True) + try: + default = getFromDict(ctd_values, lineage) + except KeyError: + continue + setInDict(ini_values, lineage, default) # write the ctd with the values taken from the dictionary out = StringIO() - ctd_tree = model.write_ctd(out, margs) + ctd_tree = ini_model.write_ctd(out, ini_values) print(out.getvalue())
--- a/generate-foo.sh Fri Nov 06 19:46:06 2020 +0000 +++ b/generate-foo.sh Thu Dec 01 19:24:40 2022 +0000 @@ -8,17 +8,15 @@ # get the tests from the CMakeLists.txt # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt # - several tools with duplicated input (leads to conflict when linking) - # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) # - some input files are originally in a subdir (degenerated cases/), but not in test-data - # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) - # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 - # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's@${DATA_DIR_SHARE}/@@g' | grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | @@ -26,19 +24,9 @@ grep -v "MaRaClusterAdapter.*-consensus_out"| grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | sed 's@degenerate_cases/@@g' | - grep -v 'TOPP_SeedListGenerator_3"' | egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | - egrep -v '"TOPP_FeatureFinderIdentification_4"' | - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/') - - -# grep -v 'FileFilter.*-spectra:select_polarity ""' | -# grep -v 'MassTraceExtractor_2.ini ' | -# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" | -# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" | -# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" | -# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" | -# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" | + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + grep -v '"TOPP_SiriusAdapter_10"') # 1st part is a dirty hack to join lines containing a single function call, e.g. # addtest(.... @@ -50,6 +38,7 @@ # >&2 echo $line test_id=$(echo "$line" | cut -d" " -f 1) tool_id=$(echo "$line" | cut -d" " -f 2) + # >&2 echo "test_id $test_id" if [[ $test_id =~ _out_?[0-9]? ]]; then >&2 echo " skip $test_id $line" continue @@ -67,7 +56,7 @@ tes=" <test>\n" line=$(fix_tmp_files "$line") line=$(unique_files "$line") - # >&2 echo $line + # >&2 echo LINE $line #if there is an ini file then we use this to generate the test #otherwise the ctd file is used #other command line parameters are inserted later into this xml @@ -77,19 +66,23 @@ else ini="ctd/$tool_id.ctd" fi + # >&2 echo "========================================================" + # >&2 echo "USING ini $ini" cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') ctdtmp=$(mktemp) - #echo python3 fill_ctd_clargs.py --ctd $ini $cli # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) - # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" - eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" - # echo $ctdtmp + # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" + eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" + # >&2 echo $ctdtmp # >&2 cat $ctdtmp testtmp=$(mktemp) - python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null + # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" + CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null + echo "<!-- $test_id -->" cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - rm $ctdtmp $testtmp + + rm "$ctdtmp" "$testtmp" #> /dev/null @@ -130,23 +123,23 @@ #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) #this function replaces the tmp file by the expected file. function fix_tmp_files { -# >&2 echo "FIX $line" + # >&2 echo "FIX $line" ret="" for a in $@; do - if [[ ! $a =~ .tmp$ ]]; then + # >&2 echo " a "$a + if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then ret="$ret $a" continue fi -# >&2 echo " a "$a - g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") -# >&2 echo " g "$g - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g) + diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") + # >&2 echo " diff_line "$diff_line + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) # >&2 echo " in1 "$in1 if [[ "$a" != "$in1" ]]; then ret="$ret $a" continue fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) in2=$(basename $in2 | sed 's/)$//') # >&2 echo " in2 "$in2 if [[ -f "test-data/$in2" ]]; then @@ -176,11 +169,11 @@ fi ln -f -s $in1 test-data/$in2 done - for i in test-data/*.tmp - do + + find test-data/ -name "*.tmp" -print0 | + while IFS= read -r -d '' i; do if [ ! -e test-data/$(basename $i .tmp) ]; then ln -s $(basename $i) test-data/$(basename $i .tmp) - #ln -s $(basename $i) test-data/$(basename $i .tmp) else ln -fs $(basename $i) test-data/$(basename $i .tmp) fi @@ -194,14 +187,14 @@ # id=$1 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" -# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | sed 's/degenerate_cases\///' | egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | grep add_test | egrep "TOPP|UTILS" | sed 's@${DATA_DIR_SHARE}/@@g;'| - sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'| + sed 's@${TMP_RIP_PATH}@./@g'| sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | while read line
--- a/generate.sh Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -#!/usr/bin/env bash - -VERSION=2.6 -FILETYPES="filetypes.txt" -PROFILE="20.05" -## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') - -export tmp=$(mktemp -d) -export CTDCONVERTER="$tmp/CTDConverter" - -############################################################################### -## reset old data -############################################################################### -# rm $(ls *xml |grep -v macros) -# rm -rf ctd -# mkdir -p ctd -# echo "" > prepare_test_data.sh - -############################################################################### -## generate tests -## also creates -## - conda environment (for executing the binaries) and -## - the git clone of OpenMS (for generating the tests) -## - ctd files -############################################################################### -bash ./test-data.sh ./macros_autotest.xml - -############################################################################### -## get the -## - conda package (for easy access and listing of the OpenMS binaries), -############################################################################### -# if [ ! -d $OPENMSPKG ]; then -# mkdir $OPENMSPKG/ -# wget -P $OPENMSPKG/ "$CONDAPKG" -# tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/ -# rm $OPENMSPKG/"$(basename $CONDAPKG)" -# fi - -############################################################################### -## Get python libaries for CTD -> Galaxy conversion -## TODO fix to main repo OR conda packkage if PRs are merged -############################################################################### -# if [ ! -d CTDopts ]; then -# # git clone https://github.com/genericworkflownodes/CTDopts CTDopts -# git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts -# fi -if [ ! -d $CTDCONVERTER ]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER -fi -# export PYTHONPATH=$(pwd)/CTDopts -############################################################################### -## conversion ctd->xml -############################################################################### - -find . -maxdepth 0 -name "[A-Z]*xml" -delete -source $(dirname $(which conda))/../etc/profile.d/conda.sh -conda activate $tmp/OpenMS$VERSION-env -python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err -if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi -conda deactivate - -patch PepNovoAdapter.xml < PepNovoAdapter.patch -patch OMSSAAdapter.xml < OMSSAAdapter.patch - -# https://github.com/OpenMS/OpenMS/pull/4984 -sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml -# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 -patch -p0 <404-urls.patch - -# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool - -# for i in A-E F-H I-L M-N O-P Q-Z -# do -# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & -# done
--- a/hardcoded_params.json Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ -{ - "#": "blacklist parameters", - - "version": [{"value": "@"}], - "debug": [{"value": "@"}], - "algorithm:debug": [{"value": "@"}], - "java_memory": [{"value": "@"}], - "java_permgen": [{"value": "@"}], - "#": "type of input is always determined from the file extension ", - "in_type": [{"value": "@"}], - - "#": "tool specific blacklist parameters", - - "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], - "NET_executable": [{ - "value": "@", - "tools": ["FileConverter"] - }], - - - "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], - - "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", - "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - "#": "TODO would need treatment as prefix-output", - "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - - "#": "hardcode parameter values", - - "comet_version": [{ - "value":"2016.01 rev. 3" - }], - "comet_executable": [{ - "value":"comet" - }], - "crux_executable": [{ - "value": "crux" - }], - "fido_executable": [{ - "value":"Fido" - }], - "fidocp_executable": [{ - "value":"FidoChooseParameters" - }], - "maracluster_executable": [{ - "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" - }], - "mascot_directory": [{ - "value":"TODO" - }], - "myrimatch_executable": [{ - "value":"myrimatch" - }], - "omssa_executable": [{ - "value":"$(dirname $(realpath $(which omssacl)))/omssacl" - }], - "ThermoRaw_executable": [{ - "value": "ThermoRawFileParser.exe", - "tools": ["FileConverter"] - }], - "pepnovo_executable": [{ - "value":"pepnovo" - }], - "percolator_executable": [{ - "value":"percolator" - }], - "xtandem_executable": [{ - "value":"xtandem" - }], - "executable": [ - { - "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar", - "tools": ["LuciphorAdapter"] - }, { - "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", - "tools": ["MSFraggerAdapter"] - }, { - "value":"$(msgf_plus -get_jar_path)", - "tools": ["MSGFPlusAdapter"] - }, { - "value": "/home/berntm/Downloads/novor/lib/novor.jar", - "tools": ["NovorAdapter"] - }, { - "value":"$(which sirius)", - "tools": ["SiriusAdapter", "AssayGeneratorMetabo"] - }, { - "value":"spectrast", - "tools": ["SpectraSTSearchAdapter"] - } - ], - "r_executable": [{ - "value":"R" - }], - "rscript_executable": [{ - "value":"Rscript" - }], - "java_executable": [{ - "value":"java" - }], - "log": [{ - "value":"log.txt" - }], - "tempDirectory": [{ - "value":"$TMP_DIR" - }], - "temp_data_directory": [{ - "value":"$TMP_DIR" - }], - "algorithm:Preprocessing:tmp_dir": [{ - "value":"$TMP_DIR" - }], - "no_progress": [{ - "value": true - }], - "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed", - "num_threads": [{ - "value":"${GALAXY_SLOTS:-1}" - }], - "threads": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - "sirius:cores": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - - "#": "hardcode the outer loop threads for OpenSwathWorkflow", - "outer_loop_threads": [{ - "value": "1", - "tools": ["OpenSwathWorkflow"] - }], - "separator": [{ - "value": ",", - "tools": ["IDMassAccuracy"] - }], - - "#": "don't alow to copy data internally to save computation time for reloading", - "copy_data": [{ - "value": "false", - "tools": ["MapAlignerTreeGuided"] - }], - - "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", - - "#": "test is not a hardcoded value since we need to set it in the tool tests", - "test": [{ - "CTD:type": "text", - "XML:type": "hidden" - }], - - "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)", - - "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools", - "out_type": [{ - "CTD:required": true, - "CTD:advanced": false - }], - - "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", - "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", - "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", - "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", - "out": [{ - "CTD:is_list": false, - "tools": ["SeedListGenerator"] - }, { - "CTD:required": true, - "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] - }, { - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["MzMLSplitter"] - }, { - "value": "@", - "tools": ["IDRipper"] - }], - - "#": "Try to remove xml data type whereever possible", - "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml", - "xml_out": [{ - "CTD:restrictions": "bioml", - "tools": ["XTandemAdapter"] - }], - - "#": "IDFileConverter remove xml", - "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", - "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", - "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", - "in": [{ - "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", - "tools": ["IDFileConverter"] - }, { - "CTD:is_list": false, - "tools": ["OpenSwathWorkflow"] - }, { - "CTD:restrictions": "idXML,mzid,xquest.xml", - "tools": ["XFDR"] - }, { - "CTD:restrictions": "mzML,idXML,featureXML", - "tools": ["SeedListGenerator"] - }], - - "#": "IDMapper has in and spectra:in params, in is used in out as format_source", - "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", - "spectra:in": [{ - "CTD:name": "_in", - "tools": ["IDMapper"] - }], - - "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527", - "#": "output-prefix", - "out_path": [{ - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "idXML", - "tools": ["IDRipper"] - }], - "outputDirectory": [{ - "CTD:type": "output-prefix", - "CTD:advanced": false, - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["OpenSwathFileSplitter"] - }], - - "#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443", - "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", - "output_files": [{ - "CTD:required": true, - "tools": ["OpenSwathDIAPreScoring"] - }, { - "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html", - "tools": ["SpectraSTSearchAdapter"] - - }] -}
--- a/macros.xml Fri Nov 06 19:46:06 2020 +0000 +++ b/macros.xml Thu Dec 01 19:24:40 2022 +0000 @@ -3,14 +3,15 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.6</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@TOOL_VERSION@">2.8</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> - <!-- makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.9.0">blast</requirement> + <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.13.0">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> @@ -21,6 +22,7 @@ <xml name="stdio"> <stdio> <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> + <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> @@ -32,23 +34,15 @@ </citations> </xml> <xml name="adv_opts_macro"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"/> - <when value="advanced"> - <yield/> - </when> - </conditional> + <section name="adv_opts" title="Advanced Options" expanded="false"> + <yield/> + </section> </xml> <!-- sanitizers and validators --> - <xml name="list_string_val"> - <validator type="regex" message="parameter must not start with $">^[^$]</validator> - - <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + <xml name="list_string_val" token_name=""> + <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> + <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> @@ -64,8 +58,8 @@ </valid> </sanitizer> </xml> - <xml name="list_float_valsan"> - <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> + <xml name="list_float_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -78,8 +72,8 @@ </valid> </sanitizer> </xml> - <xml name="list_integer_valsan"> - <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <xml name="list_integer_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -119,11 +113,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def ]]></token></macros>
--- a/macros_autotest.xml Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27205 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - <xml name="autotest_AccurateMassSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> - <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_AssayGeneratorMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="100.0"/> - <param name="max_fragment_mz" value="900.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_BaselineFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="BaselineFilter_input.mzML"/> - <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="struc_elem_length" value="1.5"/> - <param name="struc_elem_unit" value="Thomson"/> - <param name="method" value="tophat"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ClusterMassTracesByPrecursor"> -</xml> - <xml name="autotest_ClusterMassTraces"> -</xml> - <xml name="autotest_CometAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_2_prepared.mzML"/> - <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_2_in.fasta"/> - <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_3.mzML"/> - <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_3.fasta"/> - <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:1200"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> - <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovoCID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovoCID_1_input.mzML"/> - <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovo_1_input.mzML"/> - <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="PAM30MS"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_2_input.featureXML"/> - <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="average"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_3_input.consensusXML"/> - <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="6"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPIons"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.5"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_6_input.idXML"/> - <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_8_input.idXML"/> - <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusMapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="accession_filter" value=""/> - <param name="description_filter" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="algorithm_type" value="robust_regression"/> - <param name="ratio_threshold" value="0.67"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CruxAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="custom_enzyme" value=""/> - <param name="decoy_prefix" value="decoy_"/> - <param name="deisotope" value="false"/> - <param name="report_decoys" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="extra_index_args" value=""/> - <param name="extra_search_args" value=""/> - <param name="extra_percolator_args" value=""/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_mass_units" value="ppm"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="fragment_bin_width" value="0.02"/> - <param name="isotope_error" value=""/> - <param name="run_percolator" value="false"/> - <param name="enzyme" value="trypsin"/> - <param name="digestion" value="full-digest"/> - <param name="allowed_missed_cleavages" value="0"/> - <param name="decoy_format" value="peptide-reverse"/> - <param name="keep_terminal_aminos" value="NC"/> - <param name="cterm_modifications" value=""/> - <param name="nterm_modifications" value=""/> - <param name="modifications" value=""/> - <param name="test_fdr" value="0.01"/> - <param name="train_fdr" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CVInspector"> -</xml> - <xml name="autotest_DatabaseFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DatabaseSuitability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.9"/> - <param name="FDR" value="1.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="true"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.9"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_Decharger"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Decharger_input.featureXML"/> - <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="FeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="10"/> - <param name="charge_span_max" value="4"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.1"/> - <param name="potential_adducts" value=""H:+:0.7" "Na:+:0.1" "(2)H4H-4:0:0.1:-2:heavy""/> - <param name="max_neutrals" value="0"/> - <param name="max_minority_bound" value="2"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DecoyDatabase"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="true"/> - <param name="type" value="protein"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KRP"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Chymotrypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KR"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_4.fasta"/> - <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="RNA"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DeMeanderize"> -</xml> - <xml name="autotest_DigestorMotif"> -</xml> - <xml name="autotest_Digestor"> -</xml> - <xml name="autotest_DTAExtractor"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":61"/> - <param name="level" value="1,2,3"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":"/> - <param name="level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":1000"/> - <param name="rt" value=":"/> - <param name="level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_EICExtractor"> -</xml> - <xml name="autotest_Epifany"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idxml"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="false"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ERPairFinder"> -</xml> - <xml name="autotest_ExternalCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FalseDiscoveryRate"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="true"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="true"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="0.05"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="0.3"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderCentroided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - <param name="pseudo_rt_shift" value="500.0"/> - </conditional> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="intensity"> - <param name="bins" value="1"/> - </section> - <section name="mass_trace"> - <param name="mz_tolerance" value="0.02"/> - <param name="min_spectra" value="14"/> - <param name="max_missing" value="1"/> - <param name="slope_bound" value="0.1"/> - </section> - <section name="isotopic_pattern"> - <param name="charge_low" value="2"/> - <param name="charge_high" value="2"/> - <param name="mz_tolerance" value="0.02"/> - <param name="intensity_percentage" value="10.0"/> - <param name="intensity_percentage_optional" value="0.1"/> - <param name="optional_fit_improvement" value="2.0"/> - <param name="mass_window_width" value="100.0"/> - <param name="abundance_12C" value="98.93"/> - <param name="abundance_14N" value="99.632"/> - </section> - <section name="seed"> - <param name="min_score" value="0.8"/> - </section> - <section name="fit"> - <param name="max_iterations" value="500"/> - </section> - <section name="feature"> - <param name="min_score" value="0.7"/> - <param name="min_isotope_fit" value="0.8"/> - <param name="min_trace_score" value="0.5"/> - <param name="min_rt_span" value="0.333"/> - <param name="max_rt_span" value="2.5"/> - <param name="rt_shape" value="symmetric"/> - <param name="max_intersection" value="0.35"/> - <param name="reported_mz" value="monoisotopic"/> - </section> - <section name="user-seed"> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.1"/> - <param name="min_score" value="0.5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="none"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIsotopeWavelet"> -</xml> - <xml name="autotest_FeatureFinderMetaboIdent"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> - <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> - <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="mz_window" value="5.0"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_window" value="20.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="3.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="100.0"/> - <param name="chrom_peak_snr" value="0.0"/> - <param name="chrom_fwhm" value="100.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="median"/> - <param name="trace_termination_criterion" value="sample_rate"/> - <param name="trace_termination_outliers" value="2"/> - <param name="min_sample_rate" value="0.01"/> - <param name="min_trace_length" value="30.0"/> - <param name="max_trace_length" value="3000.0"/> - </section> - <section name="epd"> - <param name="enabled" value="false"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="10.0"/> - <param name="max_fwhm" value="80.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="4.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="false"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="false"/> - <param name="use_smoothed_intensities" value="false"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="true"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="max_height"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMRM"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMRM_1_input.mzML"/> - <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="min_rt_distance" value="10.0"/> - <param name="min_num_peaks_per_feature" value="5"/> - <param name="min_signal_to_noise_ratio" value="2.0"/> - <param name="write_debug_files" value="false"/> - <param name="resample_traces" value="false"/> - <param name="write_debuginfo" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMultiplex"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl8]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="90.0"/> - <param name="rt_band" value="10.0"/> - <param name="rt_min" value="5.0"/> - <param name="mz_tolerance" value="40.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.8"/> - <param name="averagine_similarity" value="0.75"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="1"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Lys8,Arg10]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="5:15"/> - <param name="isotopes_per_peptide" value="5:10"/> - <param name="rt_typical" value="45.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="200.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="RNA"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="5:15"/> - <param name="isotopes_per_peptide" value="5:10"/> - <param name="rt_typical" value="45.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="200.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="DNA"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:5"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10000000.0"/> - <param name="peptide_similarity" value="0.95"/> - <param name="averagine_similarity" value="0.8"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:5"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10000000.0"/> - <param name="peptide_similarity" value="0.95"/> - <param name="averagine_similarity" value="0.8"/> - <param name="averagine_similarity_scaling" value="1.0"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Dimethyl4]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="31.0094"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> - <param name="charge" value="1:7"/> - <param name="isotopes_per_peptide" value="3:8"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.2"/> - <param name="averagine_similarity" value="0.25"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="4"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="true"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[0][6.03705]"/> - <param name="charge" value="2:8"/> - <param name="isotopes_per_peptide" value="3:8"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="0.0"/> - <param name="rt_min" value="4.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="centroid"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:7"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.4"/> - <param name="averagine_similarity" value="0.5"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="true"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="1e-05"/> - <param name="rt_band" value="0.0"/> - <param name="rt_min" value="0.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.7"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderSuperHirn"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="false"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="true"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerLabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="false"/> - <param name="rt_pair_dist" value="-1.0"/> - <param name="rt_dev_low" value="0.4"/> - <param name="rt_dev_high" value="0.4"/> - <param name="mz_pair_dists" value="8.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="true"/> - <param name="rt_pair_dist" value="-121.0382"/> - <param name="rt_dev_low" value="123.3965"/> - <param name="rt_dev_high" value="123.3965"/> - <param name="mz_pair_dists" value="4.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledKD"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="1"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="99999"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Identical"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="With_unknown_adducts"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="Identical"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledQT"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="99999"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.5"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="1.5"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="true"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FFEval"> -</xml> - <xml name="autotest_FidoAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="true"/> - <param name="group_level" value="true"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_4_input.idXML"/> - <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_5_input.idXML"/> - <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="true"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.9"/> - <param name="peptide" value="0.01"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_2_input.someInputDTA2D"/> - <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_3_input.featureXML"/> - <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_5_input.mzML"/> - <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_6_input.mzML"/> - <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_7_input.consensusXML"/> - <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_8_input.mzML"/> - <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/> - <param name="out_type" value="mzData"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_input.consensusXML"/> - <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_11_input.peplist"/> - <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> - <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_13_input.peptides.kroenik"/> - <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_output.featureXML"/> - <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_20_input.featureXML"/> - <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_23_input.mzML"/> - <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_26_output.mzXML"/> - <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_27_input.mzML"/> - <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_28_input.mzML"/> - <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="1e-05"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_29_output.mzML"/> - <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="multiple"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_input.mzML"/> - <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="single"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_output.mzML"/> - <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_32_input.mzML"/> - <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ginkgotoxin-ms-switching.raw"/> - <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":30"/> - <param name="mz" value=":1000"/> - <param name="int" value=":20000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value="30:"/> - <param name="mz" value="1000:"/> - <param name="int" value="100:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_4_input.mzML"/> - <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="true"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":1000"/> - <param name="mz" value=":480"/> - <param name="int" value=":79000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":0.6"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":3"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value="1000:"/> - <param name="mz" value="440:"/> - <param name="int" value="70000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value="0.51:"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value="3:"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_7_input.mzML"/> - <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value="7000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_8_input.consensusXML"/> - <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value="600:1400"/> - <param name="mz" value="700:2300"/> - <param name="int" value="1100:6000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_9_input.mzML"/> - <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value="SelectedIonMonitoring"/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_10_input.mzML"/> - <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Collision-induced dissociation"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_11_input.mzML"/> - <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Plasma desorption"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_12_input.mzML"/> - <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="true"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_13_input.consensusXML"/> - <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_14_input.consensusXML"/> - <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="0 2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="true"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""YDL217C""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="true"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="1.0"/> - <param name="mz" value="0.05"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":2"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":2"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":35"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":35"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="false"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="slof"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="positive"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="negative"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43_input.mzML"/> - <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43.tmp.mzML"/> - <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_44_input.mzML"/> - <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_45_input.featureXML"/> - <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_46_input.featureXML"/> - <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="exact"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="false"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_49_input.mzML"/> - <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="true"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="slof"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileInfo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> - <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> - <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_3_input.featureXML"/> - <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_4_input.mzXML"/> - <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_5_input.mzDat"/> - <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_6_input.mzData"/> - <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="true"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_7_input.consensusXML"/> - <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_9_input.mzML"/> - <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_10_input.idXML"/> - <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_12_input.mzML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_13_input.consensusXML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_14_input.mzid"/> - <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_15_input.mzid"/> - <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_16_input.trafoXML"/> - <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_17_input.fasta"/> - <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_18_input.fasta"/> - <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value="5.0 10.0"/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="true"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="true"/> - <param name="ms_level" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> - <param name="out_type" value="featureXML"/> - <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> - <param name="out_type" value="traML"/> - <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="10.0"/> - </section> - <output_collection name="rt_concat_trafo_out" count="2"/> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_cols"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FuzzyDiff"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="whitelist" value=""<?xml-stylesheet""/> - <param name="matched_whitelist" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> - <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> - <param name="ratio" value="1.01"/> - <param name="absdiff" value="0.01"/> - <param name="verbose" value="1"/> - <param name="tab_width" value="8"/> - <param name="first_column" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_GNPSExport"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="merged_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_HighResPrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="4"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.2"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDConflictResolver"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_1_input.featureXML"/> - <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_2_input.consensusXML"/> - <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_3_input.consensusXML"/> - <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_4_input.featureXML"/> - <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="highest_intensity"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDExtractor"> -</xml> - <xml name="autotest_IDFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.pepxml"/> - <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="PepXMLFile_test.mzML"/> - <param name="mz_name" value="PepXMLFile_test"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_3_input.protXML"/> - <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_6_input1.pepXML"/> - <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value="F025589.dat.mzML"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_7_input1.xml"/> - <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_8_input.mzid"/> - <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_9_input.idXML"/> - <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="out_type" value="mzid"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_10_input.pepXML"/> - <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> - <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="PEP"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_16_input.pepXML"/> - <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_17_input.idXML"/> - <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_18_input.idXML"/> - <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_19_input.idXML"/> - <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_20_input.idXML"/> - <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_21_input.idXML"/> - <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDMapper_4_input.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.01"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_23_input.mzid"/> - <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_24_input.pep.xml"/> - <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_25_input.idXML"/> - <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_26_input.mzid"/> - <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="-1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_31_input.mzid"/> - <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_1_input.idXML"/> - <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="proteins" value="IDFilter_1_input.fas"/> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_3_input.idXML"/> - <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="peptides" value="IDFilter_3_2_input.idXML"/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_4_input.idXML"/> - <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.08"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_6_input.idXML"/> - <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="2"/> - <param name="n_protein_hits" value="10"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="true"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_7_input.idXML"/> - <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_8_input.idXML"/> - <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value="200:350"/> - <param name="mz" value="999:1000"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_9_input.idXML"/> - <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.05"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_10_input.idXML"/> - <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.3"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_11_input.idXML"/> - <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="true"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_12_input.idXML"/> - <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_12_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_13_input.idXML"/> - <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_13_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_14_input.idXML"/> - <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_14_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_15_input.idXML"/> - <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_15_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="semi"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_16_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="true"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":2"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="2:"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:3"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:0"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""calcMZ" "gt" "750.0""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""end" "ne" "23""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_2_output.consensusXML"/> - <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""Q9HP81""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_3_out.consensusXML"/> - <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.99"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_1_input.idXML"/> - <param name="in" value="IDMapper_1_input.featureXML"/> - <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_2_input.idXML"/> - <param name="in" value="IDMapper_2_input.consensusXML"/> - <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_3_input.idXML"/> - <param name="in" value="IDMapper_3_input.featureXML"/> - <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="4.0"/> - <param name="mz_tolerance" value="3.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_4_input.idXML"/> - <param name="in" value="IDMapper_4_input.featureXML"/> - <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="10.0"/> - <param name="mz_tolerance" value="20.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_4_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_5_input.idXML"/> - <param name="in" value="IDMapper_5_input.featureXML"/> - <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="20.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_5_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMassAccuracy"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="number_of_bins" value="10"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/> - <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_error_ppm" value="false"/> - <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_error_ppm" value="false"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/> - <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/> - <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="true"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/> - <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/> - <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML"/> - <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="add_to" value="IDMerger_5_input1.idXML"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/> - <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDPosteriorErrorProbability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="true"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="true"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDRipper"/> - <xml name="autotest_IDRTCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRTCalibration_1_input.idXML"/> - <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML"/> - <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDScoreSwitcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_output.idXML"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="false"/> - <param name="new_score" value="Percolator_PEP"/> - <param name="new_score_orientation" value="lower_better"/> - <param name="new_score_type" value="Posterior Error Probability"/> - <param name="old_score" value="Percolator_qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDScoreSwitcher_2_input.idXML"/> - <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="true"/> - <param name="new_score" value="Posterior Probability_score"/> - <param name="new_score_orientation" value="higher_better"/> - <param name="new_score_type" value="Posterior Probability"/> - <param name="old_score" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_InternalCalibration"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_1_BSA1.mzML"/> - <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1"/> - <param name="RT_chunking" value="-1.0"/> - <section name="cal"> - <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> - <param name="lock_require_mono" value="false"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="true"/> - <param name="threshold" value="1.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="500"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> - <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1 2 3"/> - <param name="RT_chunking" value="60.0"/> - <section name="cal"> - <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> - <param name="lock_require_mono" value="true"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="false"/> - <param name="threshold" value="10.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="70"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IsobaricAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> - <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value=""/> - <param name="reporter_mass_shift" value="0.1"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value="l1"/> - <param name="channel_115_description" value="l2"/> - <param name="channel_116_description" value="l3"/> - <param name="channel_117_description" value="lung"/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="tmt10plex"/> - <param name="in" value="MS3_nonHierarchical.mzML"/> - <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="Collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_LabeledEval"> -</xml> - <xml name="autotest_LuciphorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="LuciphorAdapter_1_input.mzML"/> - <param name="id" value="LuciphorAdapter_1_input.idXML"/> - <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="fragment_method" value="CID"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="fragment_error_units" value="Da"/> - <param name="min_mz" value="150.0"/> - <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> - <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> - <param name="decoy_mass" value="79.966331"/> - <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> - <param name="max_charge_state" value="5"/> - <param name="max_peptide_length" value="40"/> - <param name="max_num_perm" value="16384"/> - <param name="modeling_score_threshold" value="0.95"/> - <param name="scoring_threshold" value="0.0"/> - <param name="min_num_psms_model" value="1"/> - <param name="run_mode" value="0"/> - <param name="rt_tolerance" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="1"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_7_input1.idXML"/> - <output_collection name="out" count="1"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_7_input2.idXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerPoseClustering"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <output_collection name="trafo_out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/> - <output_collection name="trafo_out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerSpectrum"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="gapcost" value="1.0"/> - <param name="affinegapcost" value="0.5"/> - <param name="cutoff_score" value="0.7"/> - <param name="bucketsize" value="100"/> - <param name="anchorpoints" value="100"/> - <param name="mismatchscore" value="-5.0"/> - <param name="scorefunction" value="SteinScottImproveScore"/> - </section> - <section name="model"> - <param name="type" value="interpolated"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerTreeGuided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="trafo_out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_input.mzML"/> - <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapRTTransformer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_2_input.mzML"/> - <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/> - <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="invert" value="true"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/> - <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="true"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapStatistics"> -</xml> - <xml name="autotest_MaRaClusterAdapter"/> - <xml name="autotest_MascotAdapterOnline"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_protein_links" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Mascot_parameters"> - <param name="database" value="SwissProt"/> - <param name="search_type" value="MIS"/> - <param name="enzyme" value="Trypsin"/> - <param name="instrument" value="Default"/> - <param name="missed_cleavages" value="1"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_error_units" value="Da"/> - <param name="charges" value="1,2,3"/> - <param name="taxonomy" value="All entries"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> - <param name="mass_type" value="monoisotopic"/> - <param name="number_of_hits" value="0"/> - <param name="skip_spectrum_charges" value="false"/> - <param name="search_title" value="OpenMS_search"/> - <param name="username" value="OpenMS"/> - <param name="email" value="openmsjenkins@gmail.com"/> - </section> - <section name="Mascot_server"> - <param name="hostname" value="www.matrixscience.com"/> - <param name="host_port" value="80"/> - <param name="server_path" value=""/> - <param name="timeout" value="1500"/> - <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> - <param name="use_proxy" value="false"/> - <param name="proxy_host" value=""/> - <param name="proxy_port" value="0"/> - <param name="proxy_username" value=""/> - <param name="proxy_password" value=""/> - <param name="login" value="false"/> - <param name="username" value=""/> - <param name="password" value=""/> - <param name="use_ssl" value="false"/> - <param name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0"/> - <param name="skip_export" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MascotAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_1_input.mzData"/> - <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/> - <param name="out_type" value="mgf"/> - <param name="instrument" value="ESI-TRAP"/> - <param name="precursor_mass_tolerance" value="1.3"/> - <param name="peak_mass_tolerance" value="0.3"/> - <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> - <param name="modifications" value=""Carboxymethyl (C)""/> - <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_2_input.mascotXML"/> - <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="instrument" value="Default"/> - <param name="precursor_mass_tolerance" value="2.0"/> - <param name="peak_mass_tolerance" value="1.0"/> - <param name="taxonomy" value="All entries"/> - <param name="modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="0"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value=""/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/> - <param name="in_seq" value=""/> - <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="0 1"/> - <param name="format" value="table"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=","/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> - <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="1 2 3"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MassTraceExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="6.0"/> - <param name="max_trace_length" value="12.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteAdductDecharger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteSpectralMatcher"> -</xml> - <xml name="autotest_MetaProSIP"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_correlation_distance_to_averagine" value="-1.0"/> - <param name="pattern_15N_TIC_threshold" value="0.95"/> - <param name="pattern_13C_TIC_threshold" value="0.95"/> - <param name="pattern_2H_TIC_threshold" value="0.95"/> - <param name="pattern_18O_TIC_threshold" value="0.95"/> - <param name="heatmap_bins" value="20"/> - <param name="observed_peak_fraction" value="0.5"/> - <param name="min_consecutive_isotopes" value="2"/> - <param name="score_plot_yaxis_min" value="0.0"/> - <param name="collect_method" value="correlation_maximum"/> - <param name="lowRIA_correlation_threshold" value="-1.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_mzML" value="MetaProSIP_1_input.mzML"/> - <param name="in_fasta" value="MetaProSIP_1_input.fasta"/> - <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/> - <param name="mz_tolerance_ppm" value="10.0"/> - <param name="rt_tolerance_s" value="30.0"/> - <param name="intensity_threshold" value="10.0"/> - <param name="correlation_threshold" value="0.7"/> - <param name="xic_threshold" value="0.7"/> - <param name="decomposition_threshold" value="0.7"/> - <param name="weight_merge_window" value="5.0"/> - <param name="plot_extension" value="png"/> - <param name="qc_output_directory" value=""/> - <param name="labeling_element" value="C"/> - <param name="use_unassigned_ids" value="false"/> - <param name="use_averagine_ids" value="false"/> - <param name="report_natural_peptides" value="false"/> - <param name="filter_monoisotopic" value="false"/> - <param name="cluster" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MRMMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input.TraML"/> - <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.3"/> - <param name="product_tolerance" value="0.3"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input_2.TraML"/> - <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.01"/> - <param name="product_tolerance" value="0.01"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MRMPairFinder"> -</xml> - <xml name="autotest_MRMTransitionGroupPicker"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="true"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSFraggerAdapter"/> - <xml name="autotest_MSGFPlusAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="add_decoys" value="false"/> - <param name="legacy_conversion" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="database" value="proteins.fasta"/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error_range" value="0,1"/> - <param name="fragment_method" value="from_spectrum"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="protocol" value="none"/> - <param name="tryptic" value="fully"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="min_peptide_length" value="6"/> - <param name="max_peptide_length" value="40"/> - <param name="matches_per_spec" value="1"/> - <param name="add_features" value="false"/> - <param name="max_mods" value="2"/> - <param name="max_missed_cleavages" value="-1"/> - <param name="tasks" value="0"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSSimulator"> -</xml> - <xml name="autotest_MSstatsConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="max"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_1_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/> - <param name="method" value="LFQ"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_2_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_3_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MultiplexResolver"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_1_input.consensusXML"/> - <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> - <param name="missed_cleavages" value="1"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_2_input.consensusXML"/> - <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> - <param name="missed_cleavages" value="4"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_3_input.consensusXML"/> - <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Leu3]"/> - <param name="missed_cleavages" value="2"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_4_input.consensusXML"/> - <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> - <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="missed_cleavages" value="3"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="10"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MyriMatchAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="MinPeptideMass" value="0.0"/> - <param name="MaxPeptideMass" value="10000.0"/> - <param name="MinPeptideLength" value="5"/> - <param name="MaxPeptideLength" value="75"/> - <param name="UseSmartPlusThreeModel" value="false"/> - <param name="NumIntensityClasses" value="3"/> - <param name="ClassSizeMultiplier" value="2.0"/> - <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> - <param name="SpectrumListFilters" value=""/> - <param name="ignoreConfigErrors" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_mass_tolerance_unit" value="ppm"/> - <param name="precursor_mass_tolerance_avg" value="false"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance_unit" value="Da"/> - <param name="database" value="proteins.fasta"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="NumChargeStates" value="3"/> - <param name="TicCutoffPercentage" value="0.98"/> - <param name="MaxDynamicMods" value="2"/> - <param name="MaxResultRank" value="5"/> - <param name="CleavageRules" value=""/> - <param name="MinTerminiCleavages" value="2"/> - <param name="MaxMissedCleavages" value="-1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MzMLSplitter"/> - <xml name="autotest_MzTabExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_1_input.consensusXML"/> - <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_2_input.idXML"/> - <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_3_input.featureXML"/> - <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_out.consensusXML"/> - <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_5_in.consensusXML"/> - <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_6_input.idXML"/> - <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_7_input.consensusXML"/> - <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterGaussian"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterSGolay"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NovorAdapter"/> - <xml name="autotest_NucleicAcidSearchEngine"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="decharge_ms2" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> - <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> - <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="-2"/> - <param name="max_charge" value="-14"/> - <param name="include_unknown_charge" value="true"/> - <param name="use_avg_mass" value="false"/> - <param name="use_adducts" value="false"/> - <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> - <param name="isotopes" value="0 1 2"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="ions" value="a-B,c,w,y"/> - </section> - <section name="modifications"> - <param name="variable" value=""/> - <param name="variable_max_per_oligo" value="2"/> - <param name="resolve_ambiguities" value="false"/> - </section> - <section name="oligo"> - <param name="min_size" value="5"/> - <param name="max_size" value="0"/> - <param name="missed_cleavages" value="22"/> - <param name="enzyme" value="no cleavage"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="fdr"> - <param name="decoy_pattern" value="DECOY_"/> - <param name="cutoff" value="0.05"/> - <param name="remove_decoys" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OMSSAAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="pc" value="1"/> - <param name="hs" value="4"/> - <param name="tez" value="1"/> - <param name="tom" value="0"/> - <param name="tem" value="0"/> - <param name="tex" value="1446.94"/> - <param name="zt" value="3"/> - <param name="z1" value="0.95"/> - <param name="zc" value="1"/> - <param name="zcc" value="2"/> - <param name="zoh" value="2"/> - <param name="no" value="4"/> - <param name="nox" value="40"/> - <param name="i" value="1,4"/> - <param name="sp" value="100"/> - <param name="sb1" value="1"/> - <param name="sct" value="0"/> - <param name="x" value="0"/> - <param name="hm" value="2"/> - <param name="ht" value="6"/> - <param name="mm" value="128"/> - <param name="mnm" value="false"/> - <param name="is" value="0.0"/> - <param name="ir" value="0.0"/> - <param name="ii" value="0.0"/> - <param name="chunk_size" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="database" value="proteins.fasta"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="v" value="1"/> - <param name="enzyme" value="Trypsin"/> - <param name="hl" value="30"/> - <param name="he" value="1.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXLLF"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input.mzML"/> - <param name="database" value="OpenPepXLLF_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_xlinks" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass" value="138.0680796"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input2.mzML"/> - <param name="database" value="OpenPepXLLF_input2.fasta"/> - <param name="decoy_string" value="decoy_"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value="Carbamidomethyl (C)"/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="1"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""D" "E" "C-term""/> - <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> - <param name="mass" value="-18.010595"/> - <param name="mass_mono_link" value=""/> - <param name="name" value="DMTMM"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="1"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXL"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXL_input.mzML"/> - <param name="consensus" value="OpenPepXL_input.consensusXML"/> - <param name="database" value="OpenPepXL_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass_light" value="138.0680796"/> - <param name="mass_iso_shift" value="12.075321"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="original"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAssayGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="2,3"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="enable_ipf" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathChromatogramExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="50.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="true"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathConfidenceScoring"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> - <param name="decoys" value="1"/> - <param name="transitions" value="2"/> - <section name="GLM"> - <param name="intercept" value="3.87333466"/> - <param name="delta_rt" value="-0.02898629"/> - <param name="dist_int" value="-7.75880768"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDecoyGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.8"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.4"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="true"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> - <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDIAPreScoring"> -</xml> - <xml name="autotest_OpenSwathFeatureXMLToTSV"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="false"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathFileSplitter"/> - <xml name="autotest_OpenSwathMzMLFileCacher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> - <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="false"/> - <param name="full_meta" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathRewriteToFeatureXML"> -</xml> - <xml name="autotest_OpenSwathRTNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="true"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="3"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="3"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathWorkflow"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> - <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cacheWorkingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="true"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="550.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="true"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.2"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="none"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="true"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="sqMass"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="true"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.6666666666666666"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="true"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerHiRes"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_5_input.mzML"/> - <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="0.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value=""/> - <param name="report_FWHM" value="false"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerIterative"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_1_input.mzML"/> - <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="1.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="1.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="false"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_2_input.mzML"/> - <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="0.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="2.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="true"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerWavelet"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> - <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="2.0"/> - <param name="centroid_percentage" value="0.8"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="1.0"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="200.0"/> - <param name="peak_bound_ms2_level" value="50.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="true"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.1"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="100"/> - <section name="penalties"> - <param name="position" value="1.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PepNovoAdapter"> -</xml> - <xml name="autotest_PeptideIndexer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="true"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="0"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_2.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="full"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="semi"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="remove"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_10_input.idXML"/> - <param name="fasta" value="PeptideIndexer_10_input.fasta"/> - <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="true"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="empty.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_14.idXML"/> - <param name="fasta" value="PeptideIndexer_2.fasta"/> - <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PercolatorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2.osw"/> - <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms1"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> - <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> - <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="transition"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PhosphoScoring"> -</xml> - <xml name="autotest_PrecursorIonSelector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorIonSelector_features.featureXML"/> - <param name="ids" value="PrecursorIonSelector_ids.idXML"/> - <param name="num_precursors" value="1"/> - <param name="load_preprocessing" value="false"/> - <param name="store_preprocessing" value="false"/> - <param name="simulation" value="true"/> - <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="db_path" value="PrecursorIonSelector_db.fasta"/> - <param name="fixed_modifications" value=""/> - <section name="algorithm"> - <param name="type" value="IPS"/> - <param name="max_iteration" value="10"/> - <param name="rt_bin_capacity" value="10"/> - <param name="step_size" value="1"/> - <param name="peptide_min_prob" value="0.2"/> - <param name="sequential_spectrum_order" value="false"/> - <section name="MIPFormulation"> - <section name="thresholds"> - <param name="min_protein_probability" value="0.2"/> - <param name="min_protein_id_probability" value="0.95"/> - <param name="min_pt_weight" value="0.5"/> - <param name="min_mz" value="500.0"/> - <param name="max_mz" value="5000.0"/> - <param name="min_pred_pep_prob" value="0.5"/> - <param name="min_rt_weight" value="0.5"/> - <param name="use_peptide_rule" value="true"/> - <param name="min_peptide_ids" value="2"/> - <param name="min_peptide_probability" value="0.95"/> - </section> - <section name="combined_ilp"> - <param name="k1" value="0.2"/> - <param name="k2" value="0.2"/> - <param name="k3" value="0.4"/> - <param name="scale_matching_probs" value="true"/> - </section> - <section name="feature_based"> - <param name="no_intensity_normalization" value="false"/> - <param name="max_number_precursors_per_feature" value="1"/> - </section> - </section> - <section name="Preprocessing"> - <param name="precursor_mass_tolerance" value="0.9"/> - <param name="precursor_mass_tolerance_unit" value="Da"/> - <param name="preprocessed_db_path" value=""/> - <param name="preprocessed_db_pred_rt_path" value=""/> - <param name="preprocessed_db_pred_dt_path" value=""/> - <param name="max_peptides_per_run" value="100000"/> - <param name="missed_cleavages" value="1"/> - <param name="taxonomy" value=""/> - <param name="store_peptide_sequences" value="false"/> - <section name="rt_settings"> - <param name="min_rt" value="960.0"/> - <param name="max_rt" value="3840.0"/> - <param name="rt_step_size" value="30.0"/> - <param name="gauss_mean" value="-1.0"/> - <param name="gauss_sigma" value="3.0"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorIonSelector_features.featureXML"/> - <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="ids" value="PrecursorIonSelector_ids.idXML"/> - <param name="num_precursors" value="1"/> - <param name="load_preprocessing" value="false"/> - <param name="store_preprocessing" value="false"/> - <param name="simulation" value="false"/> - <param name="db_path" value="PrecursorIonSelector_db.fasta"/> - <param name="fixed_modifications" value=""/> - <section name="algorithm"> - <param name="type" value="IPS"/> - <param name="max_iteration" value="10"/> - <param name="rt_bin_capacity" value="10"/> - <param name="step_size" value="1"/> - <param name="peptide_min_prob" value="0.2"/> - <param name="sequential_spectrum_order" value="false"/> - <section name="MIPFormulation"> - <section name="thresholds"> - <param name="min_protein_probability" value="0.2"/> - <param name="min_protein_id_probability" value="0.95"/> - <param name="min_pt_weight" value="0.5"/> - <param name="min_mz" value="500.0"/> - <param name="max_mz" value="5000.0"/> - <param name="min_pred_pep_prob" value="0.5"/> - <param name="min_rt_weight" value="0.5"/> - <param name="use_peptide_rule" value="true"/> - <param name="min_peptide_ids" value="2"/> - <param name="min_peptide_probability" value="0.95"/> - </section> - <section name="combined_ilp"> - <param name="k1" value="0.2"/> - <param name="k2" value="0.2"/> - <param name="k3" value="0.4"/> - <param name="scale_matching_probs" value="true"/> - </section> - <section name="feature_based"> - <param name="no_intensity_normalization" value="false"/> - <param name="max_number_precursors_per_feature" value="1"/> - </section> - </section> - <section name="Preprocessing"> - <param name="precursor_mass_tolerance" value="0.9"/> - <param name="precursor_mass_tolerance_unit" value="Da"/> - <param name="preprocessed_db_path" value=""/> - <param name="preprocessed_db_pred_rt_path" value=""/> - <param name="preprocessed_db_pred_dt_path" value=""/> - <param name="max_peptides_per_run" value="100000"/> - <param name="missed_cleavages" value="1"/> - <param name="taxonomy" value=""/> - <param name="store_peptide_sequences" value="false"/> - <section name="rt_settings"> - <param name="min_rt" value="960.0"/> - <param name="max_rt" value="3840.0"/> - <param name="rt_step_size" value="30.0"/> - <param name="gauss_mean" value="-1.0"/> - <param name="gauss_sigma" value="3.0"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_charge" value="3"/> - <param name="intensity_threshold" value="-1.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> - <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="precursor_mass_tolerance" value="1.5"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinInference"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinInference_1_input.idXML"/> - <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="merge_runs" value="all"/> - <param name="annotate_indist_groups" value="true"/> - <section name="Merging"> - <param name="annotate_origin" value="false"/> - <param name="allow_disagreeing_settings" value="false"/> - </section> - <section name="Algorithm"> - <param name="min_peptides_per_protein" value="1"/> - <param name="score_aggregation_method" value="maximum"/> - <param name="treat_charge_variants_separately" value="true"/> - <param name="treat_modification_variants_separately" value="true"/> - <param name="use_shared_peptides" value="false"/> - <param name="skip_count_annotation" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinQuantifier"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="median"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_3_input.featureXML"/> - <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="mean"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="true"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="true"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.idXML"/> - <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinResolver"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="fasta" value="ProteinResolver_1_input.fasta"/> - <param name="in" value="ProteinResolver_1_input.consensusXML"/> - <param name="in_path" value=""/> - <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/> - <section name="resolver"> - <param name="missed_cleavages" value="2"/> - <param name="min_length" value="6"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="designer"> - <param name="experiment" value="ExperimentalSetting"/> - <param name="file" value="File"/> - <param name="separator" value="tab"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PSMFeatureExtractor"> -</xml> - <xml name="autotest_PTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="PTModel_1_input_positive.idXML"/> - <param name="in_negative" value="PTModel_1_input_negative.idXML"/> - <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="c" value="0.5"/> - <param name="svm_type" value="C_SVC"/> - <param name="nu" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="max_positive_count" value="1000"/> - <param name="max_negative_count" value="1000"/> - <param name="redundant" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="100.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.1"/> - <param name="nu_step_size" value="1.3"/> - <param name="nu_stop" value="0.9"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_QCCalculator"> -</xml> - <xml name="autotest_QCEmbedder"> -</xml> - <xml name="autotest_QCExporter"> -</xml> - <xml name="autotest_QCExtractor"> -</xml> - <xml name="autotest_QCImporter"> -</xml> - <xml name="autotest_QCMerger"> -</xml> - <xml name="autotest_QCShrinker"> -</xml> - <xml name="autotest_QualityControl"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="QualityControl_1_in.consensusXML"/> - <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/> - <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/> - <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="in_contaminants" value="QualityControl_1.fasta"/> - <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/> - <section name="FragmentMassError"> - <param name="unit" value="auto"/> - <param name="tolerance" value="20.0"/> - </section> - <section name="MS2_id_rate"> - <param name="assume_all_target" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNADigestor"> -</xml> - <xml name="autotest_RNAMassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""AUCGGC""/> - <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="charge" value="-1 -2"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNPxlSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="3"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="2"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNPxlXICFilter"> -</xml> - <xml name="autotest_RTEvaluation"> -</xml> - <xml name="autotest_RTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_1_input.idXML"/> - <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.1"/> - <param name="kernel_type" value="POLY"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="3000.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="RTModel_2_input_positive.idXML"/> - <param name="in_negative" value="RTModel_2_input_negative.idXML"/> - <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_3_input.idXML"/> - <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_4_input.txt" ftype="txt"/> - <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SeedListGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.mzML"/> - <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SemanticValidator"> -</xml> - <xml name="autotest_SequenceCoverageCalculator"> -</xml> - <xml name="autotest_SimpleSearchEngine"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SimpleSearchEngine_1.mzML"/> - <param name="database" value="SimpleSearchEngine_1.fasta"/> - <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Search"> - <param name="enzyme" value="Trypsin"/> - <param name="decoys" value="false"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="annotate"> - <param name="PSM" value=""/> - </section> - <section name="peptide"> - <param name="min_size" value="7"/> - <param name="max_size" value="40"/> - <param name="missed_cleavages" value="1"/> - <param name="motif" value=""/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SiriusAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_1_input.mzML"/> - <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="pubchem"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpecLibCreator"> -</xml> - <xml name="autotest_SpecLibSearcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpecLibSearcher_1.mzML"/> - <param name="lib" value="SpecLibSearcher_1.MSP"/> - <output_collection name="out" count="1"/> - <param name="compare_function" value="ZhangSimilarityScore"/> - <section name="precursor"> - <param name="mass_tolerance" value="3.0"/> - <param name="mass_tolerance_unit" value="Da"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - </section> - <section name="report"> - <param name="top_hits" value="10"/> - </section> - <section name="filter"> - <param name="remove_peaks_below_threshold" value="2.01"/> - <param name="min_peaks" value="5"/> - <param name="max_peaks" value="150"/> - <param name="cut_peaks_below" value="1000"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterBernNorm"> -</xml> - <xml name="autotest_SpectraFilterMarkerMower"> -</xml> - <xml name="autotest_SpectraFilterNLargest"> -</xml> - <xml name="autotest_SpectraFilterNormalizer"> -</xml> - <xml name="autotest_SpectraFilterParentPeakMower"> -</xml> - <xml name="autotest_SpectraFilterScaler"> -</xml> - <xml name="autotest_SpectraFilterSqrtMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterThresholdMower"> -</xml> - <xml name="autotest_SpectraFilterWindowMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="50.0"/> - <param name="peakcount" value="2"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="20.0"/> - <param name="peakcount" value="4"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraMerger"> -</xml> - <xml name="autotest_SpectraSTSearchAdapter"/> - <xml name="autotest_StaticModification"> -</xml> - <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> -</xml> - <xml name="autotest_TargetedFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="minutes"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="seconds"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> - <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> - <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="traml"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TextExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_2_input.consensusXML"/> - <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="true"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_5_input.idXML"/> - <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="true"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="true"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_6_input.featureXML"/> - <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_7_input.consensusXML"/> - <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_9_input.idXML"/> - <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="0"/> - <param name="add_hit_metavalues" value="0"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TICCalculator"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="regular"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed_parallel"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TOFCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_1_input.mzML"/> - <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="false"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_2_input.mzML"/> - <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="true"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TransformationEvaluation"> -</xml> - <xml name="autotest_XFDR"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="true"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in3.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in4.idXML"/> - <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_XMLValidator"> -</xml> - <xml name="autotest_XTandemAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="valid"/> - <param name="max_valid_expect" value="1e-14"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteinslong.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> -<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
--- a/macros_discarded_auto.xml Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,378 +0,0 @@ - -<xml name="manutest_OpenSwathFileSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <output_collection name="outputDirectory" count=""/> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test></xml> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MSFraggerAdapter"> -<test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MaRaClusterAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="verbose" value="2"/> - <param name="precursor_tolerance" value="20.0"/> - <param name="precursor_tolerance_units" value="ppm"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/> - <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/> - <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="pcut" value="-10.0"/> - <param name="min_cluster_size" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_NovorAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NovorAdapter_in.mzML"/> - <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="enzyme" value="Trypsin"/> - <param name="fragmentation" value="CID"/> - <param name="massAnalyzer" value="Trap"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="precursor_mass_tolerance" value="15.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="variable_modifications" value="Acetyl (K)"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="forbiddenResidues" value="I"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_SpectraSTSearchAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="pep.xml"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="tsv"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml>
--- a/macros_test.xml Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,545 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - -<!-- a copy of a FileConverter test without the advanced options used - in order to check if this works (all other tests enable advanced) --> -<xml name="manutest_FileConverter"> -<test expect_num_outputs="1"> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> -</test> -</xml> -<!-- tests contributed by the galaxyproteomics community --> -<xml name="manutest_ClusterMassTracesByPrecursor"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> - </test> -</xml> -<xml name="manutest_ClusterMassTraces"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> - </test> -</xml> -<xml name="manutest_CVInspector"> - <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 --> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> - <param name="cv_names" value="XLMOD"/> - <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> - <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> - <output name="html" ftype="html" value="CVInspector.html"/> - </test> -</xml> -<xml name="manutest_DeMeanderize"> - <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/> - <output name="out" ftype="mzml" value="DeMeanderize.mzml"/> - </test> -</xml> -<xml name="manutest_Digestor"> - <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random.fa"/> - <output name="out" ftype="fasta" value="Digestor.fasta"/> - <param name="out_type" value="fasta"/> - </test> -</xml> -<xml name="manutest_EICExtractor"> - <test expect_num_outputs="1"><!-- just using some random test data --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="spectra.mzML"/> - <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> - <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> - </test> -</xml> -<xml name="manutest_ERPairFinder"> - <!-- TODO --> -</xml> -<xml name="manutest_FeatureFinderIsotopeWavelet"> - <test expect_num_outputs="1"><!--just use the input of another FeatureFinder --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_FFEval"> - <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/> - <output name="out" value="FFEval.featureXML" compare="sim_size"/> - <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/> - </test> -</xml> -<xml name="manutest_IDExtractor"> - <test expect_num_outputs="1"><!-- --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> - <param name="best_hits" value="true"/> - <param name="number_of_peptides" value="1"/> - <output name="out" value="IDExtractor.idXML" compare="sim_size"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> - <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> - <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -</xml> -<xml name="manutest_LabeledEval"> - <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/> - <output name="stdout" value="LabeledEval.txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_MapStatistics"> - <test expect_num_outputs="1"><!-- test with a featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> - <output name="out" ftype="txt" value="MapStatistics.txt"/> - </test> - <test expect_num_outputs="1"><!-- test with a consensusxml input --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> - <output name="out" ftype="txt" value="MapStatistics2.txt"/> - </test> -</xml> -<xml name="manutest_MetaboliteSpectralMatcher"> - <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="database" value="MetaboliteSpectralDB.mzML"/> - <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> - </test> -</xml> -<xml name="manutest_MRMPairFinder"> - <!-- TODO no idea about a useful input for pair_in --> -</xml> -<xml name="manutest_MSSimulator"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -</xml> -<xml name="manutest_OpenSwathDIAPreScoring"> - <!-- data from a test that included all the needed test files --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output_collection name="output_files" count="1"> - <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> - - <!-- test with two inputs (actually the same file .. symlinked) --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> - <output_collection name="output_files" count="2"> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_OpenSwathFileSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> - <output_collection name="outputDirectory" count="6"> - <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> - <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> - </output_collection> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> -</xml> -<xml name="manutest_OpenSwathRewriteToFeatureXML"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="adv_opts_cond|test" value="true"/> - <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> - </test> -</xml> -<xml name="manutest_PepNovoAdapter"> - <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection - unclear https://github.com/OpenMS/OpenMS/issues/4719)--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> -</xml> -<xml name="manutest_PhosphoScoring"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> - <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> - </test> -</xml> -<xml name="manutest_PSMFeatureExtractor"> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="idxml"/> - <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/> - </test> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="mzid"/> - <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> - </test> -</xml> -<xml name="manutest_QCCalculator"> - <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> - <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> - <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> - <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> - <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> - <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> - </test> -</xml> -<xml name="manutest_QCEmbedder"> - <!--TODO--> -</xml> -<xml name="manutest_QCExporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCExtractor"> - <!--TODO--> -</xml> -<xml name="manutest_QCImporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCMerger"> - <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> - <output name="out" ftype="qcml" value="QCMerger.qcML"/> - </test> -</xml> -<xml name="manutest_QCShrinker"> - <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML"/> - <output name="out" ftype="qcml" value="QCShrinker.qcML"/> - </test> -</xml> -<xml name="manutest_RNADigestor"> - <test expect_num_outputs="1"><!--random RNAsequence input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random_RNA.fa"/> - <output name="out" ftype="fasta" value="RNADigestor.fasta"/> - </test> -</xml> -<xml name="manutest_RNPxlXICFilter"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> - </test> -</xml> -<xml name="manutest_RTEvaluation"> - <!-- just chosen an arbitrary input and autgenerated output--> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/> - <output name="out" ftype="tabular" value="RTEvaluation.tsv"/> - </test> -</xml> -<xml name="manutest_SemanticValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> - <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_SequenceCoverageCalculator"> - <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> - <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> - <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpecLibCreator"> - <!--TODO could not find test data --> -</xml> -<xml name="manutest_SpectraFilterBernNorm"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterMarkerMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNLargest"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNormalizer"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterParentPeakMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterScaler"> - <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterThresholdMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraMerger"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> - <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer"> -<!-- -TODO model_output_file creates multiple files--> -</xml> -<xml name="manutest_TransformationEvaluation"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/> - </test> -</xml> -<xml name="manutest_XMLValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- a/prepare_test_data_manual.sh Fri Nov 06 19:46:06 2020 +0000 +++ b/prepare_test_data_manual.sh Thu Dec 01 19:24:40 2022 +0000 @@ -86,10 +86,13 @@ PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr +# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Fri Nov 06 19:46:06 2020 +0000 +++ b/readme.md Thu Dec 01 19:24:40 2022 +0000 @@ -22,11 +22,14 @@ Manual updates should only be done to -- the `@GALAXY_VERSION@"` token in `macros.xml` - and the manually contributed tests in `macros_test.xml` (The goal is that all tools that do not have an automatically generated test are covered here) - the `hardcoded_params.json` files +Wrapper versions are managed in `bump.json`. For tools listed in the file +the wrapper version will be set accordingly and otherwise `0` is used. +For a major update of the tool version the bump file should be reset (to `{}`). + In a few cases patches may be acceptable. Installation @@ -71,10 +74,15 @@ Preprocessing: -- For each input / output data set parameter a directory is crated (named by - the parameter) - For input data set parameters the links to the actual location of the data - sets are created + sets are created, the link names are `element_identifier`.`EXT`, where `EXT` + is an extension that is known by OpenMS +- In order to avoid name collisions for the created links each is placed in a + unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name + of the parameter and `DATASET_ID` is the id of the Galaxy dataset +- the same happens for output parameters that are in 1:1 correspondence with + an input parameter + Main:
--- a/test-data.sh Fri Nov 06 19:46:06 2020 +0000 +++ b/test-data.sh Thu Dec 01 19:24:40 2022 +0000 @@ -1,22 +1,25 @@ #!/usr/bin/env bash -VERSION=2.6 -FILETYPES="filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" +VERSION=2.8 +FILETYPES="aux/filetypes.txt" +CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" # import the magic . ./generate-foo.sh # install conda if [ -z "$tmp" ]; then - tmp=$(mktemp -d) - created="yes" + tmp=$(mktemp -d) + created="yes" fi export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" -export OPENMSENV="$tmp/OpenMS$VERSION-env" -export CTDCONVERTER="$tmp/CTDConverter" +export OPENMSENV="OpenMS$VERSION-env" + +if [ -z "$CTDCONVERTER" ]; then + export CTDCONVERTER="$tmp/CTDConverter" +fi if [[ -z "$1" ]]; then autotests="/dev/null" @@ -25,11 +28,11 @@ fi if type conda > /dev/null; then - true + true else - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh - bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" - source "$tmp/miniconda/bin/activate" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh + bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" + source "$tmp/miniconda/bin/activate" fi eval "$(conda shell.bash hook)" @@ -42,24 +45,27 @@ echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then - git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT - cd $OPENMSGIT - git submodule init - git submodule update - cd - + # TODO >2.8 reenable original release branch .. also in else branch + # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917 + # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT + git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT + cd $OPENMSGIT + git submodule init + git submodule update + cd - else - cd $OPENMSGIT - git pull origin release/$VERSION.0 - cd - + cd $OPENMSGIT + git pull origin release/$VERSION.0-plus + cd - fi echo "Create OpenMS $VERSION conda env" # TODO currently add lxml (needed by CTDConverter) # TODO for some reason a to recent openjdk is used if conda env list | grep "$OPENMSENV"; then - true + true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -69,10 +75,10 @@ echo "Download OpenMS $VERSION package $CONDAPKG" if [[ ! -d $OPENMSPKG ]]; then - mkdir $OPENMSPKG - wget -q -P $OPENMSPKG/ "$CONDAPKG" - tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ - rm $OPENMSPKG/"$(basename $CONDAPKG)" + mkdir $OPENMSPKG + wget -q -P $OPENMSPKG/ "$CONDAPKG" + tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ + rm $OPENMSPKG/"$(basename $CONDAPKG)" fi ############################################################################### @@ -81,40 +87,46 @@ ############################################################################### echo "Clone CTDConverter" if [[ ! -d $CTDCONVERTER ]]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER + #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter + git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER else - cd $CTDCONVERTER - git pull origin topic/cdata - cd - + cd $CTDCONVERTER + git pull origin topic/fix-selects2 + cd - fi +conda activate $OPENMSENV +cd $CTDCONVERTER +python -m pip install . --no-deps +cd - +conda deactivate -############################################################################### -## copy all the test data files to test-data -## most of it (outputs) will be overwritten later, but its needed for -## prepare_test_data -############################################################################### + +# ############################################################################### +# ## copy all the test data files to test-data +# ## most of it (outputs) will be overwritten later, but its needed for +# ## prepare_test_data +# ############################################################################### echo "Get test data" -find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ -if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then - wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML - mv MetaboliteSpectralDB.mzML test-data/ +if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then + wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv if [ ! -d test-data/pepnovo_models/ ]; then - mkdir -p /tmp/pepnovo - wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip PepNovo.20120423.zip -d /tmp/pepnovo/ - mv /tmp/pepnovo/Models test-data/pepnovo_models/ - rm PepNovo.20120423.zip - rm -rf /tmp/pepnovo + mkdir -p /tmp/pepnovo + wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip + unzip PepNovo.20120423.zip -d /tmp/pepnovo/ + mv /tmp/pepnovo/Models test-data/pepnovo_models/ + rm PepNovo.20120423.zip + rm -rf /tmp/pepnovo fi ############################################################################### ## generate ctd files using the binaries in the conda package @@ -124,17 +136,13 @@ rm -rf ctd mkdir -p ctd -# TODO because of https://github.com/OpenMS/OpenMS/issues/4641 -# this needs to be done from within test-data -cd test-data for i in $OPENMSPKG/bin/* do - b=$(basename $i) - echo $b - $b -write_ctd ../ctd/ - sed -i -e 's/²/^2/' ../ctd/$b.ctd + b=$(basename $i) + echo $b + $b -write_ctd ctd/ + sed -i -e 's/²/^2/' ctd/$b.ctd done -cd - ############################################################################### ## fix ini files: OpenMS test data contains ini files with outdated ini files. ## e.g. variables might be in different nodes, outdated variables present, new @@ -146,17 +154,17 @@ echo "Update test INI files" for ini in test-data/*ini do - tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') - bin=$(which $tool) - if [[ -z $bin ]]; then + tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') + bin=$(which $tool) + if [[ -z $bin ]]; then >&2 echo "missing binary to convert $ini" - continue - fi - cp $ini $ini.backup - $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr - if [[ "$?" -ne "0" ]]; then - >&2 echo "could not convert $ini" - fi + continue + fi + cp $ini $ini.backup + $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr + if [[ "$?" -ne "0" ]]; then + >&2 echo "could not convert $ini" + fi done ############################################################################### @@ -185,17 +193,17 @@ prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -# prepare_test_data > tmp_test_data.sh -# # remove calls not needed for the tools listed in any .list file -# echo LIST $LIST -# if [ ! -z "$LIST" ]; then -# REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -# else -# REX=".*" -# fi -# echo REX $REX -# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -# rm tmp_test_data.sh +## prepare_test_data > tmp_test_data.sh +## # remove calls not needed for the tools listed in any .list file +## echo LIST $LIST +## if [ ! -z "$LIST" ]; then +## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') +## else +## REX=".*" +## fi +## echo REX $REX +## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh +## rm tmp_test_data.sh echo "Execute test shell script" chmod u+x prepare_test_data.sh @@ -204,14 +212,13 @@ cd - || exit -############################################################################### -## create/update test data for the manually generated tests -## - run convert once with the manual tests only and -## - update test-data (needs to run 2x) -############################################################################### +# ############################################################################### +# ## create/update test data for the manually generated tests +# ## - run convert once with the manual tests only and +# ## - update test-data (needs to run 2x) +# ############################################################################### echo "Execute test shell script for manually curated tests" chmod u+x prepare_test_data_manual.sh - cd ./test-data || exit ../prepare_test_data_manual.sh cd - || exit @@ -220,22 +227,28 @@ ############################################################################### ## auto generate tests ############################################################################### + echo "Write test macros to $autotests" echo "<macros>" > "$autotests" -for i in $(ls *xml |grep -v macros) + +for i in $(ls ctd/*ctd) do - b=$(basename "$i" .xml) - get_tests2 "$b" >> "$autotests" + b=$(basename "$i" .ctd) + get_tests2 "$b" >> "$autotests" done echo "</macros>" >> "$autotests" -echo "Create test data links" -link_tmp_files +# echo "Create test data links" +# Breaks DecoyDatabase +# link_tmp_files # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests -# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator +# TODO reevaluate in >2.8 +# - https://github.com/OpenMS/OpenMS/pull/5873 +# - https://github.com/OpenMS/OpenMS/pull/5912 # # Furthermore we remove tests for tools without binaries in conda # -> MSFragger MaRaClusterAdapter NovorAdapter @@ -243,23 +256,23 @@ # not able to specify composite test data # -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then - echo "" > macros_discarded_auto.xml - for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter - do - echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml - xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml - echo "</xml>" >> macros_discarded_auto.xml - xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp - mv tmp macros_autotest.xml - done - >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" + echo "" > macros_discarded_auto.xml + for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter + do + echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml + xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml + echo "</xml>" >> macros_discarded_auto.xml + xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp + mv tmp macros_autotest.xml + done + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate ## remove broken symlinks in test-data find test-data/ -xtype l -delete -# if [ ! -z "$created" ]; then -# echo "Removing temporary directory" -# rm -rf "$tmp" -# fi +if [ ! -z "$created" ]; then + echo "Removing temporary directory" + rm -rf "$tmp" +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pepnovo_models.loc Thu Dec 01 19:24:40 2022 +0000 @@ -0,0 +1,13 @@ +#name value path +default_models CID_IT_TRYP ${__HERE__}/pepnovo_models/ +default_models LTQ_COMP ${__HERE__}/pepnovo_models/ +default_models DBC4_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG5 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG6 ${__HERE__}/pepnovo_models/ +default_models ITDNV_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_SCORE ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG3 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DNVPART ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG4 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DB ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_CSP ${__HERE__}/pepnovo_models/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random.fa Thu Dec 01 19:24:40 2022 +0000 @@ -0,0 +1,18 @@ +>RND24402 Randomly generated sequence, created by ExPASy tool RandSeq, using average amino acid composition +LALLTDKYSVTKSIKGYAGQQQKCTDDEGLAEDSAAMSLVPIRAAWTISVSVDLFYLGIV +TNVTKDSVEHLVGIPLVTHEFMASRCEMRGQVVSATFGSWQKAESKAYRIPLKATPLDEF +VESAVYLFGGSSNEYECVLIGNSHPVLIFLDIDAVPGARKPRTGFFMAEGFHSKGETRAL +VGKSPPLGEYRKGAFHFTFPIKEAIRLGPPKKRIMGYRDALEGGLNHYVQTQVLVLLPMI +QVARRWENGLGLLVGKFLKLPTHPLDLNQVTLCWSEAVTEDNKRFLLTIKTSAQGKSAPT +SHINYVPQHNSMELMAINGSPFAAQHKSNDEIESMRDLSKLYADAETLESHGERGVRHQA +TETKISKVTNLRRKLPQLLDLNVVDNACNWESVGAHVLEYVLVNLYLKELQEPKVELQPR +LNETTMKAGASSLGVESGASAHSFYKGGVSEAKLRFRHVATPAAARIWWCVVMFRINRRY +DGITYNSVGEQLSGVHEYVRAAQLFGLTTGKNLRSTGIVIIKLSTAIDLECLVQAKPKEA +YVLANDYIGAKPHPARLETGPALVLFIVETINNDTLNAAILITALGGKFLNVRPDLLFGV +QALFGCVRMFRHADCTIGREKFVQTEISHKAKFLYEINEFFLERILQFEEAKSPVGAPAY +DIPIGRGLVMDSSTDLWNIYVVELISGQEKRTGIDPDTPMGTSHNLYMTDARLDERDQRS +FLNSEFVKPSKLANGSEWADPYVEPDKTEVIAFFPATLIVIMADGSALNGQVCIQPAKDN +SKMADDLATVHIGQDRPCDWGISASHEYDEVNRPARINGVMMQQLMAEDNQGPGASPRDQ +MGDADDLKEIKWNKYVIDNEIIGRERGISAERVKIFLGDTLTARGLLDSPPGQTKVFDLR +PRQSDKNQSGMFKRDQNAMYFPLEYDRIGAQTDTGSLYSTLITKFASISIDLVKLSMPRE +KQIDEERLHSEFIENQKRSALPAVQKNLACISCVEACRGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_RNA.fa Thu Dec 01 19:24:40 2022 +0000 @@ -0,0 +1,2 @@ +> random RNA +GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU
--- a/tools_blacklist.txt Fri Nov 06 19:46:06 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426 -# DigestorMotif - -# deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html -# https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html -IDDecoyProbability - -# personal communication with author V. Bafna: -# "InsPect is no longer maintained as there are many better tools including MS-GF+" -InspectAdapter - -# licence? see https://github.com/bioconda/bioconda-recipes/issues/18953 -#MSFraggerAdapter - -# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727 -ProteomicsLFQ - -# https://github.com/OpenMS/OpenMS/issues/4401 -InclusionExclusionListCreator -RTPredict -PTPredict