annotate DigestorMotif.xml @ 0:d2ba97751d56 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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: [Utilities]-->
<tool id="DigestorMotif" name="DigestorMotif" version="2.1.0">
  <description>digests a protein database in-silico</description>
  <macros>
    <token name="@EXECUTABLE@">DigestorMotif</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>DigestorMotif

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_missed_cleavages:
  -missed_cleavages $param_missed_cleavages
#end if
#if $param_mass_accuracy:
  -mass_accuracy $param_mass_accuracy
#end if
#if $param_min_length:
  -min_length $param_min_length
#end if
#if $param_out_option:
  -out_option $param_out_option
#end if
#if $param_enzyme:
  -enzyme $param_enzyme
#end if
#if $param_motif:
  -motif     "$param_motif"
#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="fasta" optional="False" label="FASTA input file" help="(-in) "/>
    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/>
    <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/>
    <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/>
    <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="CNBr">CNBr</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="proline endopeptidase">proline endopeptidase</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="V8-DE">V8-DE</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="V8-E">V8-E</option>
      <option value="Asp-N">Asp-N</option>
      <option value="PepsinA">PepsinA</option>
      <option value="no cleavage">no cleavage</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="TrypChymo">TrypChymo</option>
    </param>
    <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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" format="idxml"/>
  </outputs>
  <help>digests a protein database in-silico


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