Mercurial > repos > galaxyp > openms_peptideindexer
diff PeptideIndexer.xml @ 14:0693b186f39e 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 21:45:45 +0000 |
| parents | d6aca689dd48 |
| children |
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--- a/PeptideIndexer.xml Thu Dec 01 19:11:03 2022 +0000 +++ b/PeptideIndexer.xml Fri Jun 14 21:45:45 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: [ID Processing]--> +<!--Proposed Tool Section: [Identification 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> + <description>Refreshes the protein references for all peptide hits</description> <macros> <token name="@EXECUTABLE@">PeptideIndexer</token> <import>macros.xml</import> @@ -15,10 +14,10 @@ ## 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)' && #if $fasta: mkdir fasta && - ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && + cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && #end if mkdir out && @@ -47,17 +46,17 @@ <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="-in" type="data" format="idxml" 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)"> + <param argument="-decoy_string_position" type="select" 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=""> + <param argument="-missing_decoy_action" type="select" 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> @@ -66,19 +65,36 @@ <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=""> + <param argument="-unmatched_action" type="select" 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="-aaa_max" type="integer" 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" 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"/> + <param argument="-allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/> <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"> + <param name="name" argument="-enzyme:name" type="select" 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="Trypsin">Trypsin</option> <option value="Arg-C">Arg-C</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="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="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</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> @@ -89,31 +105,15 @@ <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="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</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)"> + <param name="specificity" argument="-enzyme:specificity" type="select" 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> @@ -123,7 +123,7 @@ </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=""> + <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> @@ -137,7 +137,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_PeptideIndexer_1 --> + <tests> + <!-- TOPP_PeptideIndexer_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -145,7 +146,7 @@ </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"/> + <output name="out" value="PeptideIndexer_1_out.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"/> @@ -156,6 +157,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -166,6 +168,9 @@ <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_PeptideIndexer_2 --> <test expect_num_outputs="2"> @@ -175,7 +180,7 @@ </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"/> + <output name="out" value="PeptideIndexer_2_out.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"/> @@ -186,6 +191,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -196,6 +202,9 @@ <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_PeptideIndexer_3 --> <test expect_num_outputs="2"> @@ -205,7 +214,7 @@ </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"/> + <output name="out" value="PeptideIndexer_3_out.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"/> @@ -216,6 +225,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -226,6 +236,9 @@ <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_PeptideIndexer_4 --> <test expect_num_outputs="2"> @@ -235,7 +248,7 @@ </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"/> + <output name="out" value="PeptideIndexer_4_out.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"/> @@ -246,6 +259,7 @@ <param name="aaa_max" value="0"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -256,6 +270,9 @@ <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_PeptideIndexer_5 --> <test expect_num_outputs="2"> @@ -265,7 +282,7 @@ </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"/> + <output name="out" value="PeptideIndexer_5_out.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"/> @@ -276,6 +293,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -286,6 +304,9 @@ <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_PeptideIndexer_6 --> <test expect_num_outputs="2"> @@ -295,7 +316,7 @@ </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"/> + <output name="out" value="PeptideIndexer_6_out.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"/> @@ -306,6 +327,7 @@ <param name="aaa_max" value="3"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -316,6 +338,9 @@ <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_PeptideIndexer_7 --> <test expect_num_outputs="2"> @@ -325,7 +350,7 @@ </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"/> + <output name="out" value="PeptideIndexer_7_out.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"/> @@ -336,6 +361,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="full"/> @@ -346,6 +372,9 @@ <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_PeptideIndexer_8 --> <test expect_num_outputs="2"> @@ -355,7 +384,7 @@ </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"/> + <output name="out" value="PeptideIndexer_8_out.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"/> @@ -366,6 +395,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="semi"/> @@ -376,6 +406,9 @@ <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_PeptideIndexer_9 --> <test expect_num_outputs="2"> @@ -385,7 +418,7 @@ </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"/> + <output name="out" value="PeptideIndexer_9_out.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"/> @@ -396,6 +429,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -406,6 +440,9 @@ <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_PeptideIndexer_10 --> <test expect_num_outputs="2"> @@ -415,7 +452,7 @@ </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"/> + <output name="out" value="PeptideIndexer_10_output.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"/> @@ -426,6 +463,7 @@ <param name="aaa_max" value="3"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="true"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="auto"/> @@ -436,6 +474,9 @@ <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_PeptideIndexer_12 --> <test expect_num_outputs="2"> @@ -445,7 +486,7 @@ </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"/> + <output name="out" value="PeptideIndexer_12_out.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"/> @@ -456,6 +497,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -466,6 +508,9 @@ <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_PeptideIndexer_13 --> <test expect_num_outputs="2"> @@ -473,9 +518,9 @@ <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="empty.idXML"/> + <param name="in" value="empty_0.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"/> + <output name="out" value="empty_1.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"/> @@ -486,6 +531,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="auto"/> @@ -496,6 +542,9 @@ <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_PeptideIndexer_14 --> <test expect_num_outputs="2"> @@ -505,7 +554,7 @@ </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"/> + <output name="out" value="PeptideIndexer_14_out.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"/> @@ -516,6 +565,7 @@ <param name="aaa_max" value="4"/> <param name="mismatches_max" value="0"/> <param name="IL_equivalent" value="false"/> + <param name="allow_nterm_protein_cleavage" value="true"/> <section name="enzyme"> <param name="name" value="auto"/> <param name="specificity" value="none"/> @@ -526,11 +576,14 @@ <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[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> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeptideIndexer.html]]></help> <expand macro="references"/> </tool>