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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="Digestor" name="Digestor" version="1.12.0">
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3 <description>Digests a protein database in-silico.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">Digestor</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>Digestor
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -out_type ${param_out_type}
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15 -missed_cleavages ${param_missed_cleavages}
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16 -min_length ${param_min_length}
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17 -max_length ${param_max_length}
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18 -enzyme ${param_enzyme}
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19 -threads \${GALAXY_SLOTS:-24}
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20 </command>
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21 <inputs>
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22 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in)"/>
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23 <param name="param_out_type" type="select" optional="True" label="Set this if you cannot control the filename of 'out', e.g., in TOPPAS." help="(-out_type)">
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24 <option value="idXML">idXML</option>
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25 <option value="fasta">fasta</option>
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26 </param>
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27 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages)"/>
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28 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length)"/>
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29 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length)"/>
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30 <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme)">
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31 <option value="Trypsin">Trypsin</option>
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32 <option value="none">none</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="param_out" label="Output file (peptides)" format="fasta">
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37 <change_format>
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38 <when input="param_out_type" value="idXML" format="idXML"/>
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39 </change_format>
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40 </data>
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41 </outputs>
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42 <help>**What it does**
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43
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44 Digests a protein database in-silico.
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45
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46
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html
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48
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49 @REFERENCES@
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50 </help>
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51 </tool>
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