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

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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: [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>
  <macros>
    <token name="@EXECUTABLE@">ConsensusID</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_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(["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
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

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
#if $in_cond.in_select == "no"
${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
#else
'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
#end if
-out
'out/output.${in_cond.in[0].ext}'

## Postprocessing
&& mv 'out/output.${in_cond.in[0].ext}' '$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>
    <conditional name="in_cond">
      <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" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
      </when>
      <when value="yes">
        <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" 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" 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" 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" 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" 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" 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" 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" 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" 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" 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>
    </param>
  </inputs>
  <outputs>
    <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 -->
    <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="6"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="identity"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.5"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="true"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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" 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">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="true"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <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 https://openms.de/doxygen/release/3.1.0/html/TOPP_ConsensusID.html]]></help>
  <expand macro="references"/>
</tool>