Mercurial > repos > galaxyp > openms_msstatsconverter
view MSstatsConverter.xml @ 5:d0a7080ddf67 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:33:43 +0000 |
parents | e3fb590554fd |
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<!--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: [File Converter]--> <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Converter to input for MSstats</description> <macros> <token name="@EXECUTABLE@">MSstatsConverter</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir in_design && cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && mkdir out && ## advanced options #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames && #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} #else cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && #end if #end if ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -in_design 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' -out 'out/output.${gxy2omsext("csv")}' ## advanced options #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: -reannotate_filenames #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} #else 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' #end if #end if ## Postprocessing && mv 'out/output.${gxy2omsext("csv")}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> <configfiles> <inputs name="args_json" data_style="paths"/> <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/> <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/> <param argument="-method" type="select" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help=""> <option value="LFQ" selected="true">LFQ</option> <option value="ISO">ISO</option> <expand macro="list_string_san" name="method"/> </param> <param argument="-msstats_bioreplicate" type="text" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help=""> <expand macro="list_string_san" name="msstats_bioreplicate"/> </param> <param argument="-msstats_condition" type="text" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help=""> <expand macro="list_string_san" name="msstats_condition"/> </param> <param argument="-msstats_mixture" type="text" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help=""> <expand macro="list_string_san" name="msstats_mixture"/> </param> <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/> <expand macro="adv_opts_macro"> <conditional name="reannotate_filenames_cond"> <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames"> <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="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> </when> <when value="yes"> <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> </when> </conditional> <param argument="-retention_time_summarization_method" type="select" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)"> <option value="manual">manual</option> <option value="max" selected="true">max</option> <option value="min">min</option> <option value="mean">mean</option> <option value="sum">sum</option> <expand macro="list_string_san" name="retention_time_summarization_method"/> </param> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" 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> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests> <!-- TOPP_MSstatsConverter_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="retention_time_summarization_method" value="max"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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" value="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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_MSstatsConverter_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="retention_time_summarization_method" value="manual"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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" value="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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_MSstatsConverter_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="retention_time_summarization_method" value="manual"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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" value="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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[Converter to input for MSstats For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSstatsConverter.html]]></help> <expand macro="references"/> </tool>