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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="Digestor" name="Digestor" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_out_type:
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19 -out_type
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20 #if " " in str($param_out_type):
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21 "$param_out_type"
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22 #else
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23 $param_out_type
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24 #end if
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25 #end if
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26 #if $param_missed_cleavages:
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27 -missed_cleavages $param_missed_cleavages
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28 #end if
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29 #if $param_min_length:
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30 -min_length $param_min_length
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31 #end if
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32 #if $param_max_length:
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33 -max_length $param_max_length
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34 #end if
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35 #if $param_enzyme:
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36 -enzyme
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37 #if " " in str($param_enzyme):
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38 "$param_enzyme"
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39 #else
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40 $param_enzyme
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41 #end if
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42 #end if
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43 -threads \${GALAXY_SLOTS:-24}
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44 #if $adv_opts.adv_opts_selector=='advanced':
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45 #if $adv_opts.param_force:
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46 -force
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47 #end if
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48 #end if
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49 </command>
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50 <inputs>
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51 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/>
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52 <param name="param_out_type" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS">
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53 <option value="idXML">idXML</option>
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54 <option value="fasta">fasta</option>
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55 </param>
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56 <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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57 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/>
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58 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/>
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59 <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) ">
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60 <option value="Trypsin">Trypsin</option>
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61 <option value="none">none</option>
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62 </param>
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63 <expand macro="advanced_options">
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64 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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65 </expand>
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66 </inputs>
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67 <outputs>
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68 <data name="param_out" format="fasta"/>
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69 </outputs>
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70 <help>**What it does**
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71
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72 Digests a protein database in-silico.
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73
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74
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help>
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76 <expand macro="references"/>
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77 </tool>
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