annotate ConsensusID.xml @ 8:4e77b8f12cd3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

<?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="2.2.0">
  <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 $param_algorithm:
  -algorithm
  #if " " in str($param_algorithm):
    "$param_algorithm"
  #else
    $param_algorithm
  #end if
#end if
#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 $param_PEPMatrix_matrix:
  -PEPMatrix:matrix
  #if " " in str($param_PEPMatrix_matrix):
    "$param_PEPMatrix_matrix"
  #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 name="param_in" type="data" format="idxml,featurexml,consensusxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help="(-rt_delta) "/>
    <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help="(-mz_delta) "/>
    <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" 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">
      <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>
    </param>
    <param name="param_filter_considered_hits" type="integer" min="0" optional="True" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help="(-considered_hits) "/>
    <param name="param_filter_min_support" type="float" min="0.0" max="1.0" optional="True" 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="(-min_support) "/>
    <param name="param_filter_count_empty" display="radio" type="boolean" truevalue="-filter:count_empty" falsevalue="" checked="false" optional="True" label="Count empty ID runs (i.e" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
    <param name="param_PEPIons_mass_tolerance" type="float" min="0.0" optional="True" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help="(-mass_tolerance) "/>
    <param name="param_PEPIons_min_shared" type="integer" min="1" optional="True" 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="(-min_shared) "/>
    <param name="param_PEPMatrix_matrix" display="radio" type="select" optional="False" value="identity" label="Substitution matrix to use for alignment-based similarity scoring" help="(-matrix) ">
      <option value="identity" selected="true">identity</option>
      <option value="PAM30MS">PAM30MS</option>
    </param>
    <param name="param_PEPMatrix_penalty" type="integer" min="1" optional="True" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help="(-penalty) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" metadata_source="param_in" format="input"/>
  </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>