Mercurial > repos > galaxyp > openms_peptideindexer
view PeptideIndexer.xml @ 13:d6aca689dd48 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:11:03 +0000 |
parents | d8ee5700c66b |
children | 0693b186f39e |
line wrap: on
line source
<?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: [ID Processing]--> <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Refreshes the protein references for all peptide hits.</description> <macros> <token name="@EXECUTABLE@">PeptideIndexer</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 $fasta: mkdir fasta && ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && #end if mkdir out && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__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 $fasta: -fasta 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' #end if -out 'out/output.${gxy2omsext("idxml")}' ## Postprocessing && mv 'out/output.${gxy2omsext("idxml")}' '$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="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> <param argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> <expand macro="list_string_san" name="decoy_string"/> </param> <param argument="-decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> <option value="prefix" selected="true">prefix</option> <option value="suffix">suffix</option> <expand macro="list_string_san" name="decoy_string_position"/> </param> <param argument="-missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> <option value="error" selected="true">error</option> <option value="warn">warn</option> <option value="silent">silent</option> <expand macro="list_string_san" name="missing_decoy_action"/> </param> <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> <param argument="-unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> <option value="error" selected="true">error</option> <option value="warn">warn</option> <option value="remove">remove</option> <expand macro="list_string_san" name="unmatched_action"/> </param> <param argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> <param argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> <param argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> <section name="enzyme" title="" help="" expanded="false"> <param name="name" argument="-enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> <option value="auto" selected="true">auto</option> <option value="Arg-C">Arg-C</option> <option value="Arg-C/P">Arg-C/P</option> <option value="Asp-N">Asp-N</option> <option value="Asp-N/B">Asp-N/B</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> <option value="Lys-N">Lys-N</option> <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> <option value="V8-E">V8-E</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="proline endopeptidase">proline endopeptidase</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="iodosobenzoate">iodosobenzoate</option> <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> <option value="no cleavage">no cleavage</option> <option value="unspecific cleavage">unspecific cleavage</option> <option value="Lys-C/P">Lys-C/P</option> <option value="PepsinA">PepsinA</option> <option value="TrypChymo">TrypChymo</option> <option value="Trypsin">Trypsin</option> <expand macro="list_string_san" name="name"/> </param> <param name="specificity" argument="-enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> <option value="auto" selected="true">auto</option> <option value="full">full</option> <option value="semi">semi</option> <option value="none">none</option> <expand macro="list_string_san" name="specificity"/> </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="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_PeptideIndexer_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> <!-- TOPP_PeptideIndexer_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> <!-- TOPP_PeptideIndexer_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_1.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_1.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_2.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_3.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_3.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_9 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> <!-- TOPP_PeptideIndexer_10 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="PeptideIndexer_1.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_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="empty.idXML"/> <param name="fasta" value="PeptideIndexer_1.fasta"/> <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta_frac="0.7" 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> <!-- TOPP_PeptideIndexer_14 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <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_frac="0.7" 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> </tests> <help><![CDATA[Refreshes the protein references for all peptide hits. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help> <expand macro="references"/> </tool>