Mercurial > repos > galaxyp > openms_openswathchromatogramextractor
diff OpenSwathChromatogramExtractor.xml @ 13:f78d734b7c01 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:13:34 +0000 |
parents | 71555764c24a |
children | 92ecd10e5c03 |
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--- a/OpenSwathChromatogramExtractor.xml Fri Nov 06 19:56:22 2020 +0000 +++ b/OpenSwathChromatogramExtractor.xml Thu Dec 01 19:13:34 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: [Targeted Experiments]--> -<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Extract chromatograms (XIC) from a MS2 map file.</description> <macros> <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -16,8 +14,13 @@ #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($in_cond.in.ext)' && +#end if mkdir tr && ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && #if $rt_norm: @@ -33,7 +36,11 @@ python3 '$__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($in_cond.in.ext)' +#end if -tr 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' #if $rt_norm: @@ -53,35 +60,46 @@ <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 separated by blank" help=" select mzml data sets(s)"/> - <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> - <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/> - <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/> - <param name="rt_window" argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/> - <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/> - <param name="mz_window" argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/> - <param name="ppm" argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/> - <param name="is_swath" argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/> - <param name="extract_MS1" argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/> + <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 separated by blank" help=" select mzml data sets(s)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> + </when> + </conditional> + <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> + <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/> + <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/> + <param argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/> + <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/> + <param argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/> + <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/> + <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/> + <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/> <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" selected="true">linear</option> <option value="b_spline">b_spline</option> <option value="interpolated">interpolated</option> <option value="lowess">lowess</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="type"/> </param> <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/> </section> <expand macro="adv_opts_macro"> - <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help=""> + <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help=""> <option value="tophat" selected="true">tophat</option> <option value="bartlett">bartlett</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="extraction_function"/> </param> - <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"> @@ -94,13 +112,161 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_OpenSwathChromatogramExtractor"/> - <expand macro="manutest_OpenSwathChromatogramExtractor"/> + <tests><!-- TOPP_OpenSwathChromatogramExtractor_test_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" 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> + <!-- TOPP_OpenSwathChromatogramExtractor_test_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + </conditional> + <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_frac="0.7" 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> + <!-- TOPP_OpenSwathChromatogramExtractor_test_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" 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> + <!-- TOPP_OpenSwathChromatogramExtractor_test_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" 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> + <!-- TOPP_OpenSwathChromatogramExtractor_test_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" 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> </tests> <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help> <expand macro="references"/> </tool>