Mercurial > repos > galaxyp > openms_multiplexresolver
diff MultiplexResolver.xml @ 14:53b202a738c3 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 21:32:24 +0000 |
| parents | 021fdb80f204 |
| children |
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--- a/MultiplexResolver.xml Thu Dec 01 19:14:58 2022 +0000 +++ b/MultiplexResolver.xml Fri Jun 14 21:32:24 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: [Utilities]--> +<!--Proposed Tool Section: [Quantitation]--> <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Completes peptide multiplets and resolves conflicts within them.</description> + <description>Completes peptide multiplets and resolves conflicts within them</description> <macros> <token name="@EXECUTABLE@">MultiplexResolver</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 $in_blacklist: mkdir in_blacklist && - ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && + cp '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && #end if mkdir out && #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -60,36 +59,36 @@ <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" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/> + <param argument="-in" type="data" format="consensusxml" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/> <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/> <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false"> - <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> + <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> <expand macro="list_string_san" name="labels"/> </param> - <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> - <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/> - <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/> - <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/> + <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> + <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/> + <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/> + <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/> </section> <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false"> - <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> - <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> - <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> - <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> - <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> - <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> - <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> - <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> - <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> - <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> - <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> - <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> - <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> - <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> + <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> + <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> + <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> + <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> + <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> + <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> + <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> + <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> + <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> + <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> + <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> + <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> + <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> + <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> </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> @@ -107,15 +106,16 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_MultiplexResolver_1 --> + <tests> + <!-- TOPP_MultiplexResolver_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="MultiplexResolver_1_input.consensusXML"/> - <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out_conflicts" value="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> <param name="missed_cleavages" value="1"/> @@ -145,16 +145,19 @@ <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> - <!-- UTILS_MultiplexResolver_2 --> + <!-- TOPP_MultiplexResolver_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="MultiplexResolver_2_input.consensusXML"/> - <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out_conflicts" value="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> <param name="missed_cleavages" value="4"/> @@ -184,16 +187,19 @@ <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> - <!-- UTILS_MultiplexResolver_3 --> + <!-- TOPP_MultiplexResolver_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="MultiplexResolver_3_input.consensusXML"/> - <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out_conflicts" value="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[][Leu3]"/> <param name="missed_cleavages" value="2"/> @@ -223,8 +229,11 @@ <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> - <!-- UTILS_MultiplexResolver_4 --> + <!-- TOPP_MultiplexResolver_4 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> @@ -232,8 +241,8 @@ </section> <param name="in" value="MultiplexResolver_4_input.consensusXML"/> <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> - <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out_conflicts" value="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl6]"/> <param name="missed_cleavages" value="3"/> @@ -263,11 +272,14 @@ <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[Completes peptide multiplets and resolves conflicts within them. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MultiplexResolver.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MultiplexResolver.html]]></help> <expand macro="references"/> </tool>