comparison ProteinResolver.xml @ 0:3070d71e0e5c draft

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0:3070d71e0e5c

<?xml version='1.0' encoding='UTF-8'?>
<tool id="ProteinResolver" name="ProteinResolver" version="2.0.0">
  <description>protein inference</description>
  <macros>
    <token name="@EXECUTABLE@">ProteinResolver</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinResolver

#if $param_fasta:
  -fasta $param_fasta
#end if
-in
  #for token in $param_in:
    $token
  #end for
#if $param_in_path:
  -in_path     "$param_in_path"
#end if
#if $param_design:
  -design $param_design
#end if
#if $param_protein_groups:
  -protein_groups $param_protein_groups
#end if
#if $param_peptide_table:
  -peptide_table $param_peptide_table
#end if
#if $param_protein_table:
  -protein_table $param_protein_table
#end if
#if $param_additional_info:
  -additional_info $param_additional_info
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $param_resolver_missed_cleavages:
  -resolver:missed_cleavages $param_resolver_missed_cleavages
#end if
#if $param_resolver_min_length:
  -resolver:min_length $param_resolver_min_length
#end if
#if $param_resolver_enzyme:
  -resolver:enzyme
  #if " " in str($param_resolver_enzyme):
    "$param_resolver_enzyme"
  #else
    $param_resolver_enzyme
  #end if
#end if
#if $param_designer_experiment:
  -designer:experiment     "$param_designer_experiment"
#end if
#if $param_designer_file:
  -designer:file     "$param_designer_file"
#end if
#if $param_designer_separator:
  -designer:separator
  #if " " in str($param_designer_separator):
    "$param_designer_separator"
  #else
    $param_designer_separator
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_fasta" type="data" format="fasta" optional="False" label="Input database file" help="(-fasta) "/>
    <param name="param_in" type="data" format="consensusxml,idxml" multiple="true" optional="True" size="30" label="Input file(s) holding experimental data" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_in_path" type="text" size="30" label="Path to idXMLs or consensusXMLs files" help="(-in_path) Ignored if 'in' is given">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_design" type="data" format="txt" optional="True" label="Text file containing the experimental design" help="(-design) See documentation for specific format requirements"/>
    <param name="param_resolver_missed_cleavages" type="integer" min="0" optional="True" value="2" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
    <param name="param_resolver_min_length" type="integer" min="1" optional="True" value="6" label="Minimum length of peptide" help="(-min_length) "/>
    <param name="param_resolver_enzyme" type="select" optional="True" value="Trypsin" label="Digestion enzyme" help="(-enzyme) ">
      <option value="Trypsin">Trypsin</option>
      <option value="none">none</option>
    </param>
    <param name="param_designer_experiment" type="text" size="30" value="ExperimentalSetting" label="Identifier for the experimental design" help="(-experiment) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_designer_file" type="text" size="30" value="File" label="Identifier for the file name" help="(-file) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_designer_separator" type="select" optional="True" value="tab" label="Separator, which should be used to split a row into columns" help="(-separator) ">
      <option value="tab">tab</option>
      <option value="semi-colon">semi-colon</option>
      <option value="comma">comma</option>
      <option value="whitespace">whitespace</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_protein_groups" format="tabular"/>
    <data name="param_peptide_table" format="tabular"/>
    <data name="param_protein_table" format="tabular"/>
    <data name="param_additional_info" format="tabular"/>
  </outputs>
  <help>**What it does**

protein inference


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help>
  <expand macro="references"/>
</tool>