annotate IDFileConverter.xml @ 2:5588e443a7db draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254

<?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="IDFileConverter" name="IDFileConverter" version="2.1.0">
  <description>Converts identification engine file formats.</description>
  <macros>
    <token name="@EXECUTABLE@">IDFileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[
   
  ## check input file type
  #set $in_type = $param_in.ext

  ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
  ln -s '$param_in' 'param_in.${in_type}' &&
  
  IDFileConverter

  #if $param_in:
    -in 'param_in.${in_type}'
  #end if
  #if $param_out:
    -out $param_out
  #end if
  #if $param_out_type:
    -out_type
    #if " " in str($param_out_type):
      "$param_out_type"
    #else
      $param_out_type
    #end if
  #end if
  #if $param_mz_file:
    -mz_file $param_mz_file
  #end if
  #if $param_mz_name:
    -mz_name     "$param_mz_name"
  #end if
  #if $param_peptideprophet_analyzed:
    -peptideprophet_analyzed
  #end if
  #if $param_score_type:
    -score_type
    #if " " in str($param_score_type):
      "$param_score_type"
    #else
      $param_score_type
    #end if
  #end if
  #if $adv_opts.adv_opts_selector=='advanced':
      #if $adv_opts.param_ignore_proteins_per_peptide:
    -ignore_proteins_per_peptide
  #end if
      #if $adv_opts.param_scan_regex:
    -scan_regex     "$adv_opts.param_scan_regex"
  #end if
      #if $adv_opts.param_force:
    -force
  #end if
  #end if
 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
    <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
      <option value="idXML">idXML</option>
      <option value="mzid">mzid</option>
      <option value="pepXML">pepXML</option>
      <option value="FASTA">FASTA</option>
    </param>
    <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/>
    <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_peptideprophet_analyzed" display="radio" type="boolean" truevalue="-peptideprophet_analyzed" falsevalue="" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results"/>
    <param name="param_score_type" display="radio" type="select" optional="False" value="qvalue" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="(-score_type) ">
      <option value="qvalue" selected="true">qvalue</option>
      <option value="PEP">PEP</option>
      <option value="score">score</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_ignore_proteins_per_peptide" display="radio" type="boolean" truevalue="-ignore_proteins_per_peptide" falsevalue="" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain" help="(-ignore_proteins_per_peptide) e.g. &quot;+1&quot; in references column, &lt;br&gt;but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
      <param name="param_scan_regex" type="text" size="30" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="(-scan_regex) See documentation for details">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <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" auto_format="true"/>
  </outputs>
  <help>Converts identification engine file formats.


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