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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:18:55 +0000 |
parents | bb1e75938909 |
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<?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="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Compute peptide and protein abundances</description> <macros> <token name="@EXECUTABLE@">ProteinQuantifier</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 && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $protein_groups: mkdir protein_groups && ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && #end if #if $design: mkdir design && ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir peptide_out && #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir mztab && #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)' #if $protein_groups: -protein_groups 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' #end if #if $design: -design 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out 'out/output.${gxy2omsext("csv")}' #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -peptide_out 'peptide_out/output.${gxy2omsext("csv")}' #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -mztab 'mztab/output.${gxy2omsext("mztab")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out/output.${gxy2omsext("csv")}' '$out' #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out' #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab' #end if #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,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help=""> <option value="median" selected="true">median</option> <option value="mean">mean</option> <option value="weighted_mean">weighted_mean</option> <option value="sum">sum</option> <expand macro="list_string_san" name="average"/> </param> <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/> <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/> <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/> <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false"> <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/> <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> </section> <section name="format" title="Output formatting options" help="" expanded="false"> <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help=""> <expand macro="list_string_san" name="separator"/> </param> <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> <option value="none">none</option> <option value="double" selected="true">double</option> <option value="escape">escape</option> <expand macro="list_string_san" name="quoting"/> </param> <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> <expand macro="list_string_san" name="replacement"/> </param> </section> <expand macro="adv_opts_macro"> <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"> <option value="out_FLAG">out (Output file for protein abundances)</option> <option value="peptide_out_FLAG">peptide_out (Output file for peptide abundances)</option> <option value="mztab_FLAG">mztab (Output file (mzTab))</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="csv"> <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="peptide_out" label="${tool.name} on ${on_string}: peptide_out" format="csv"> <filter>OPTIONAL_OUTPUTS is not None and "peptide_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="mztab" label="${tool.name} on ${on_string}: mztab" format="mztab"> <filter>OPTIONAL_OUTPUTS is not None and "mztab_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> <filter>OPTIONAL_OUTPUTS is None</filter> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_ProteinQuantifier_1 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.featureXML"/> <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_2 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.featureXML"/> <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_3 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_3_input.featureXML"/> <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_5 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_6 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_7 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_8 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_9 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_12 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_13 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_ProteinQuantifier_14 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.idXML"/> <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" 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> </tests> <help><![CDATA[Compute peptide and protein abundances For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help> <expand macro="references"/> </tool>