annotate IDFileConverter.xml @ 9:83cf7a4cd03c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

<?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 CTDConverter.-->
<!--Proposed Tool Section: [ID Processing]-->
<tool id="IDFileConverter" name="IDFileConverter" version="2.3.0">
  <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 detect_errors="aggressive"><![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_no_spectra_data_override:
  -no_spectra_data_override
#end if
    #if $adv_opts.param_add_ionmatch_annotation:
  -add_ionmatch_annotation $adv_opts.param_add_ionmatch_annotation
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" 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="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) 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_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
      <param name="param_add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="(-add_ionmatch_annotation) Will take quite some while. Match tolerance is .4"/>
      <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 https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDFileConverter.html</help>
</tool>