view IDFileConverter.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="IDFileConverter" name="IDFileConverter" version="1.12.0">
  <description>Converts identification engine file formats.</description>
  <macros>
    <token name="@EXECUTABLE@">IDFileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDFileConverter

-in ${param_in}
-out ${param_out}
-out_type ${param_out_type}
-mz_file ${param_mz_file}
-mz_name ${param_mz_name}
${param_use_precursor_data}
${param_peptideprophet_analyzed}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    ${adv_opts.param_ignore_proteins_per_peptide}
    -scan_regex ${adv_opts.param_scan_regex}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="pepXML,idXML" optional="False" label="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#mascotXML: Single Mascot XML file.#br#omssaXML: Single OMSSA XML file.#br#XTandem: Single XML file.#br#idXML: Single idXML file.#br#" help="(-in)"/>
    <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content#br#" 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="mzML,mzXML" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file)"/>
    <param name="param_mz_name" type="text" size="20" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." help="(-mz_name)"/>
    <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data true" falsevalue="-use_precursor_data false" checked="false" optional="True" label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." help="(-use_precursor_data)"/>
    <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed true" falsevalue="-peptideprophet_analyzed false" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results." help="(-peptideprophet_analyzed)"/>
    <expand macro="advanced_options">
      <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide true" falsevalue="-ignore_proteins_per_peptide false" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain e.g. &quot;+1&quot; in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" help="(-ignore_proteins_per_peptide)"/>
      <param name="param_scan_regex" type="text" size="20" label="[mascotXML only] Regular expression used to extract the scan number or retention time. See documentation for details." help="(-scan_regex)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file" format="pepXML">
      <change_format>
        <when input="param_out_type" value="idXML" format="idXML"/>
      </change_format>
    </data>
  </outputs>
  <help>**What it does**

Converts identification engine file formats.


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

@REFERENCES@
</help>
</tool>