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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="DigestorMotif" name="DigestorMotif" 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@">DigestorMotif</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>DigestorMotif
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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_missed_cleavages:
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19 -missed_cleavages $param_missed_cleavages
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20 #end if
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21 #if $param_mass_accuracy:
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22 -mass_accuracy $param_mass_accuracy
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23 #end if
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24 #if $param_min_length:
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25 -min_length $param_min_length
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26 #end if
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27 #if $param_out_option:
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28 -out_option $param_out_option
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29 #end if
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30 #if $param_enzyme:
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31 -enzyme "$param_enzyme"
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32 #end if
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33 #if $param_motif:
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34 -motif "$param_motif"
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35 #end if
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36 -threads \${GALAXY_SLOTS:-24}
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37 #if $adv_opts.adv_opts_selector=='advanced':
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38 #if $adv_opts.param_force:
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39 -force
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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44 <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/>
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45 <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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46 <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/>
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47 <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/>
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48 <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) "/>
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49 <param name="param_enzyme" type="text" size="30" value="Trypsin" label="the digestion enzyme" help="(-enzyme) ">
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50 <sanitizer>
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51 <valid initial="string.printable">
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52 <remove value="'"/>
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53 <remove value="""/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) ">
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58 <sanitizer>
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59 <valid initial="string.printable">
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60 <remove value="'"/>
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61 <remove value="""/>
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62 </valid>
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63 </sanitizer>
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64 </param>
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65 <expand macro="advanced_options">
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66 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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67 </expand>
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68 </inputs>
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69 <outputs>
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70 <data name="param_out" format="idxml"/>
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71 </outputs>
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72 <help>**What it does**
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73
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74 digests a protein database in-silico
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75
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76
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77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
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78 <expand macro="references"/>
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79 </tool>
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