Mercurial > repos > galaxyp > openms_featurefinderidentification
diff FeatureFinderIdentification.xml @ 16:65bdfab68571 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:44:29 +0000 |
| parents | 5dc928c83939 |
| children |
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--- a/FeatureFinderIdentification.xml Thu Dec 01 19:24:30 2022 +0000 +++ b/FeatureFinderIdentification.xml Fri Jun 14 21:44:29 2024 +0000 @@ -1,8 +1,7 @@ -<?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: [Quantitation]--> <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Detects features in MS1 data based on peptide identifications.</description> + <description>Detects features in MS1 data based on peptide identifications</description> <macros> <token name="@EXECUTABLE@">FeatureFinderIdentification</token> <import>macros.xml</import> @@ -15,12 +14,12 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && #if $id_ext: mkdir id_ext && - ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' && + cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' && #end if mkdir out && #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -35,11 +34,13 @@ #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir svm_xval_out && #end if +## advanced options #if $adv_opts.candidates_in: mkdir adv_opts.candidates_in && - ln -s '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' && + cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' && #end if + ## Main program call set -o pipefail && @@ -72,10 +73,12 @@ -svm:xval_out 'svm_xval_out/output.${gxy2omsext("csv")}' #end if +## advanced options #if $adv_opts.candidates_in: -candidates_in 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' #end if + #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if @@ -102,73 +105,80 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/> - <param argument="-id" type="data" format="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/> + <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/> + <param argument="-id" type="data" format="idxml" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/> <param argument="-id_ext" type="data" format="idxml" optional="true" label="Input file: 'External' peptide identifications" help="(e.g. from aligned runs) select idxml data sets(s)"/> <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/> + <param argument="-min_psm_cutoff" type="text" value="none" label="Minimum score for the best PSM of a spectrum to be used as seed" help="Use 'none' for no cutoff"> + <expand macro="list_string_san" name="min_psm_cutoff"/> + </param> + <param argument="-add_mass_offset_peptides" type="float" min="0.0" value="0.0" label="If for every peptide (or seed) also an offset peptide is extracted (true)" help="Can be used to downstream to determine MBR false transfer rates. (0.0 = disabled)"/> <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false"> - <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/> - <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/> - <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/> - <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/> - <param name="rt_quantile" argument="-extract:rt_quantile" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/> - <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/> + <param name="batch_size" argument="-extract:batch_size" type="integer" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/> + <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/> + <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/> + <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/> + <param name="rt_quantile" argument="-extract:rt_quantile" type="float" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/> + <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/> </section> <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false"> - <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/> - <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/> - <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/> - <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" optional="true" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/> + <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/> + <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/> + <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/> + <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/> </section> <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false"> - <param name="samples" argument="-svm:samples" type="integer" optional="true" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/> + <param name="samples" argument="-svm:samples" type="integer" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/> <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/> - <param name="kernel" argument="-svm:kernel" type="select" optional="true" label="SVM kernel" help=""> + <param name="kernel" argument="-svm:kernel" type="select" label="SVM kernel" help=""> <option value="RBF" selected="true">RBF</option> <option value="linear">linear</option> <expand macro="list_string_san" name="kernel"/> </param> - <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/> - <param name="log2_C" argument="-svm:log2_C" type="text" optional="true" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="xval" argument="-svm:xval" type="integer" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/> + <param name="log2_C" argument="-svm:log2_C" type="text" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_float_valsan" name="log2_C"/> </param> - <param name="log2_gamma" argument="-svm:log2_gamma" type="text" optional="true" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="log2_gamma" argument="-svm:log2_gamma" type="text" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_float_valsan" name="log2_gamma"/> </param> - <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/> - <param name="cache_size" argument="-svm:cache_size" type="float" optional="true" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/> + <param name="log2_p" argument="-svm:log2_p" type="text" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0" label="Values to try for the SVM parameter 'epsilon' during parameter optimization (epsilon-SVR only)" help="A value 'x' is used as 'epsilon = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_float_valsan" name="log2_p"/> + </param> + <param name="epsilon" argument="-svm:epsilon" type="float" min="0.0" value="0.001" label="Stopping criterion" help=""/> + <param name="cache_size" argument="-svm:cache_size" type="float" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/> <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/> - <param name="predictors" argument="-svm:predictors" type="text" optional="true" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help=""> + <param name="predictors" argument="-svm:predictors" type="text" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help=""> <expand macro="list_string_san" name="predictors"/> </param> - <param name="min_prob" argument="-svm:min_prob" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/> + <param name="min_prob" argument="-svm:min_prob" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/> </section> <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false"> - <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help=""> + <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help=""> <option value="symmetric" selected="true">symmetric</option> <option value="asymmetric">asymmetric</option> <option value="none">none</option> <expand macro="list_string_san" name="type"/> </param> - <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> + <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/> <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/> <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/> <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> - <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/> - <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> - <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> - <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> + <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/> + <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> + <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> + <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> </section> </section> <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false"> - <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/> + <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/> <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/> <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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -198,7 +208,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_FeatureFinderIdentification_1 --> + <tests> + <!-- TOPP_FeatureFinderIdentification_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -206,8 +217,10 @@ </section> <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_1.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="quantify_decoys" value="false"/> + <param name="min_psm_cutoff" value="none"/> + <param name="add_mass_offset_peptides" value="0.0"/> <section name="extract"> <param name="batch_size" value="5000"/> <param name="mz_window" value="0.1"/> @@ -229,6 +242,7 @@ <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="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/> <param name="epsilon" value="0.001"/> <param name="cache_size" value="100.0"/> <param name="no_shrinking" value="false"/> @@ -258,6 +272,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FeatureFinderIdentification_3 --> <test expect_num_outputs="2"> @@ -267,8 +284,10 @@ </section> <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_3.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="quantify_decoys" value="false"/> + <param name="min_psm_cutoff" value="none"/> + <param name="add_mass_offset_peptides" value="0.0"/> <section name="extract"> <param name="batch_size" value="5000"/> <param name="mz_window" value="0.1"/> @@ -290,6 +309,7 @@ <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="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/> <param name="epsilon" value="0.001"/> <param name="cache_size" value="100.0"/> <param name="no_shrinking" value="false"/> @@ -319,6 +339,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FeatureFinderIdentification_5 --> <test expect_num_outputs="3"> @@ -328,9 +351,11 @@ </section> <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_5.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> - <output name="candidates_out" file="FeatureFinderIdentification_5_candidates.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="candidates_out" value="FeatureFinderIdentification_5_candidates.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="quantify_decoys" value="false"/> + <param name="min_psm_cutoff" value="none"/> + <param name="add_mass_offset_peptides" value="0.0"/> <section name="extract"> <param name="batch_size" value="10"/> <param name="mz_window" value="0.1"/> @@ -352,6 +377,7 @@ <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="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/> <param name="epsilon" value="0.001"/> <param name="cache_size" value="100.0"/> <param name="no_shrinking" value="false"/> @@ -381,11 +407,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Detects features in MS1 data based on peptide identifications. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIdentification.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIdentification.html]]></help> <expand macro="references"/> </tool>