<?xml version='1.0' encoding='UTF-8'?>
<tool id="DigestorMotif" name="DigestorMotif" version="2.0.0">
  <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

#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
-threads \${GALAXY_SLOTS:-24} 
#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="text" size="30" value="Trypsin" label="the digestion enzyme" help="(-enzyme) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </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" 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>**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</help>
  <expand macro="references"/>
</tool>