view Digestor.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="Digestor" name="Digestor" version="2.0.0">
    <description>Digests a protein database in-silico.</description>
    <macros>
      <token name="@EXECUTABLE@">Digestor</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>Digestor

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if &quot; &quot; in str($param_out_type):
    &quot;$param_out_type&quot;
  #else
    $param_out_type
  #end if
#end if
#if $param_missed_cleavages:
  -missed_cleavages $param_missed_cleavages
#end if
#if $param_min_length:
  -min_length $param_min_length
#end if
#if $param_max_length:
  -max_length $param_max_length
#end if
#if $param_enzyme:
  -enzyme
  #if &quot; &quot; in str($param_enzyme):
    &quot;$param_enzyme&quot;
  #else
    $param_enzyme
  #end if
#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 format="fasta" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-out_type) e.g., in TOPPAS" label="Set this if you cannot control the filename of 'out'," name="param_out_type" optional="True" type="select">
        <option value="idXML">idXML</option>
        <option value="fasta">fasta</option>
      </param>
      <param help="(-missed_cleavages) " label="The number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/>
      <param help="(-min_length) " label="Minimum length of peptide" name="param_min_length" type="integer" value="6"/>
      <param help="(-max_length) " label="Maximum length of peptide" name="param_max_length" type="integer" value="40"/>
      <param help="(-enzyme) " label="The type of digestion enzyme" name="param_enzyme" optional="True" type="select" value="Trypsin">
        <option value="no cleavage">no cleavage</option>
        <option value="Arg-C">Arg-C</option>
        <option value="Lys-C">Lys-C</option>
        <option value="PepsinA">PepsinA</option>
        <option value="leukocyte elastase">leukocyte elastase</option>
        <option value="unspecific cleavage">unspecific cleavage</option>
        <option value="V8-DE">V8-DE</option>
        <option value="CNBr">CNBr</option>
        <option value="Chymotrypsin">Chymotrypsin</option>
        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
        <option value="Asp-N_ambic">Asp-N_ambic</option>
        <option value="2-iodobenzoate">2-iodobenzoate</option>
        <option value="proline endopeptidase">proline endopeptidase</option>
        <option value="Formic_acid">Formic_acid</option>
        <option value="TrypChymo">TrypChymo</option>
        <option value="Asp-N">Asp-N</option>
        <option value="Trypsin/P">Trypsin/P</option>
        <option value="Lys-C/P">Lys-C/P</option>
        <option value="V8-E">V8-E</option>
        <option value="Trypsin">Trypsin</option>
      </param>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>Digests a protein database in-silico.


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