<?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 CTD2Galaxy.-->
  <!--Proposed Tool Section: [ID Processing]-->
  <tool id="ConsensusID" name="ConsensusID" version="2.0.0">
    <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="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>ConsensusID

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_rt_delta:
  -rt_delta $param_rt_delta
#end if
#if $param_mz_delta:
  -mz_delta $param_mz_delta
#end if
#if $param_algorithm:
  -algorithm
  #if &quot; &quot; in str($param_algorithm):
    &quot;$param_algorithm&quot;
  #else
    $param_algorithm
  #end if
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_filter_considered_hits:
  -filter:considered_hits $param_filter_considered_hits
#end if
#if $param_filter_min_support:
  -filter:min_support $param_filter_min_support
#end if
#if $param_filter_count_empty:
  -filter:count_empty
#end if
#if $param_PEPIons_mass_tolerance:
  -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance
#end if
#if $param_PEPIons_min_shared:
  -PEPIons:min_shared $param_PEPIons_min_shared
#end if
#if $param_PEPMatrix_matrix:
  -PEPMatrix:matrix
  #if &quot; &quot; in str($param_PEPMatrix_matrix):
    &quot;$param_PEPMatrix_matrix&quot;
  #else
    $param_PEPMatrix_matrix
  #end if
#end if
#if $param_PEPMatrix_penalty:
  -PEPMatrix:penalty $param_PEPMatrix_penalty
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml,consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-rt_delta) " label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" min="0.0" name="param_rt_delta" optional="True" type="float" value="0.1"/>
      <param help="(-mz_delta) " label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" min="0.0" name="param_mz_delta" optional="True" type="float" value="0.1"/>
      <param help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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" label="Algorithm used for consensus scoring" name="param_algorithm" optional="True" type="select" value="PEPMatrix">
        <option value="PEPMatrix">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>
      </param>
      <param help="(-considered_hits) " label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" min="0" name="param_filter_considered_hits" optional="True" type="integer" value="0"/>
      <param help="(-min_support) " label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" max="1.0" min="0.0" name="param_filter_min_support" optional="True" type="float" value="0.0"/>
      <param checked="false" falsevalue="" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?" label="Count empty ID runs (i.e" name="param_filter_count_empty" optional="True" truevalue="-filter:count_empty" type="boolean"/>
      <param help="(-mass_tolerance) " label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" min="0.0" name="param_PEPIons_mass_tolerance" optional="True" type="float" value="0.5"/>
      <param help="(-min_shared) " label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" min="1" name="param_PEPIons_min_shared" optional="True" type="integer" value="2"/>
      <param help="(-matrix) " label="Substitution matrix to use for alignment-based similarity scoring" name="param_PEPMatrix_matrix" optional="True" type="select" value="identity">
        <option value="identity">identity</option>
        <option value="PAM30MS">PAM30MS</option>
      </param>
      <param help="(-penalty) " label="Alignment gap penalty (the same value is used for gap opening and extension)" min="1" name="param_PEPMatrix_penalty" optional="True" type="integer" value="5"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="input" metadata_source="param_in" name="param_out"/>
    </outputs>
    <help>Computes a consensus of peptide identifications of several identification engines.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html</help>
  </tool>