openms_consensusid: ConsensusID.xml comparison

comparison ConsensusID.xml @ 19:91da6dd00bbc 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 21:45:07 +0000
parents	f4be248c3d47
children

comparison

equal deleted inserted replaced

-:f4be248c3d47
+:91da6dd00bbc
-<?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="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-<description>Computes a consensus of peptide identifications of several identification engines.</description>
+<description>Computes a consensus of peptide identifications of several identification engines</description>
 <macros>
 <token name="@EXECUTABLE@">ConsensusID</token>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 ## Preprocessing
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 ## Main program call
 <param name="in_select" type="select" label="Run tool in batch mode for -in">
 <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="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+<param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
 </when>
 <when value="yes">
-<param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="false" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+<param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
 </when>
 </conditional>
-<param argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
+<param argument="-rt_delta" type="float" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
-<param argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
+<param argument="-mz_delta" type="float" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
 <param argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>
-<param argument="-algorithm" type="select" optional="true" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
+<param argument="-algorithm" type="select" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
 <option value="PEPMatrix" selected="true">PEPMatrix</option>
 <option value="PEPIons">PEPIons</option>
 <option value="best">best</option>
 <option value="worst">worst</option>
 <option value="average">average</option>
 <option value="ranks">ranks</option>
 <expand macro="list_string_san" name="algorithm"/>
 </param>
 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
-<param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
+<param name="considered_hits" argument="-filter:considered_hits" type="integer" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
-<param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
+<param name="min_support" argument="-filter:min_support" type="float" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
 <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
 <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>
 </section>
 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
-<param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
+<param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
-<param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
+<param name="min_shared" argument="-PEPIons:min_shared" type="integer" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
 </section>
 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
-<param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="true" label="Substitution matrix to use for alignment-based similarity scoring" help="">
+<param name="matrix" argument="-PEPMatrix:matrix" type="select" label="Substitution matrix to use for alignment-based similarity scoring" help="">
 <option value="identity">identity</option>
 <option value="PAM30MS" selected="true">PAM30MS</option>
 <expand macro="list_string_san" name="matrix"/>
 </param>
-<param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
+<param name="penalty" argument="-PEPMatrix:penalty" type="integer" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" 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>
 <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>
 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
 </data>
 </outputs>
-<tests><!-- TOPP_ConsensusID_1 -->
+<tests>
+<!-- TOPP_ConsensusID_1 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_1_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="PEPMatrix"/>
 <section name="filter">
 <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_ConsensusID_2 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_2_input.featureXML"/>
 </conditional>
-<output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="average"/>
 <section name="filter">
 <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_ConsensusID_3 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_3_input.consensusXML"/>
 </conditional>
-<output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+<output name="out" value="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="best"/>
 <section name="filter">
 <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_ConsensusID_4 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_1_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="PEPMatrix"/>
 <section name="filter">
 <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_ConsensusID_5 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_1_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="PEPIons"/>
 <section name="filter">
 <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_ConsensusID_6 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_1_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="false"/>
 <param name="algorithm" value="best"/>
 <section name="filter">
 <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_ConsensusID_7 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_6_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="true"/>
 <param name="algorithm" value="best"/>
 <section name="filter">
 <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_ConsensusID_8 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="ConsensusID_8_input.idXML"/>
 </conditional>
-<output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="rt_delta" value="0.1"/>
 <param name="mz_delta" value="0.1"/>
 <param name="per_spectrum" value="true"/>
 <param name="algorithm" value="best"/>
 <section name="filter">
 <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[Computes a consensus of peptide identifications of several identification engines.
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusID.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ConsensusID.html]]></help>
 <expand macro="references"/>
 </tool>

Mercurial > repos > galaxyp > openms_consensusid

comparison ConsensusID.xml @ 19:91da6dd00bbc draft default tip