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<?xml version='1.0' encoding='UTF-8'?>
<tool id="DigestorMotif" name="DigestorMotif" version="1.12.0">
  <description>digests a protein database in-silico</description>
  <macros>
    <token name="@EXECUTABLE@">DigestorMotif</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>DigestorMotif

-in ${param_in}
-out ${param_out}
-missed_cleavages ${param_missed_cleavages}
-mass_accuracy ${param_mass_accuracy}
-min_length ${param_min_length}
-out_option ${param_out_option}
-enzyme ${param_enzyme}
-motif ${param_motif}
-threads \${GALAXY_SLOTS:-24} 
</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 ppb" 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="text" size="20" value="Trypsin" label="the digestion enzyme" help="(-enzyme)"/>
    <param name="param_motif" type="text" size="20" value="M" label="the motif for the restricted peptidome" help="(-motif)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file (peptides)#br#" format="idXML"/>
  </outputs>
  <help>**What it does**

digests a protein database in-silico


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

@REFERENCES@
</help>
</tool>