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1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
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2
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2 <requirements>
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5
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3 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
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2
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4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
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5 </requirements>
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6
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7 <description>Converts a mascot results file to pepXML</description>
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8
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9 <command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb
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10 $input_file
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11
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12 -o $output
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13
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14 #if $database.source_select=="built_in":
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15 -d $database.dbkey
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16 #else
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17 -d $database.fasta_file
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18 #end if
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19
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20 #if $explicit_enzyme.explicit_enzyme_use
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21 --enzyme $explicit_enzyme.enzyme
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22 #end if
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23
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24 $shortid
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25
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26 </command>
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27 <inputs>
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28
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29
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30 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
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31
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32 <conditional name="database">
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33 <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
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34 <option value="built_in">Built-In</option>
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35 <option value="input_ref">Uploaded fasta file</option>
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36 </param>
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37 <when value="built_in">
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38 <param name="dbkey" type="select" format="text" >
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39 <label>Database</label>
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40 <options from_file="pepxml_databases.loc">
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41 <column name="name" index="0" />
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42 <column name="value" index="2" />
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43 </options>
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44 </param>
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45 </when>
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46 <when value="input_ref">
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47 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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48 </when>
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49 </conditional>
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50
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51 <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
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52
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53 <conditional name="explicit_enzyme">
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54 <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
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55 <when value="false" />
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56 <when value="true">
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57 <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
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58 </when>
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59 </conditional>
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60
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61
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2
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62
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63 </inputs>
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64 <outputs>
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65 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
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66 </outputs>
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67
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68 <tests>
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69 <test>
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70 <param name="source_select" value="input_ref"/>
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71 <param name="fasta_file" value="bsa.fasta"/>
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72 <param name="input_file" value="F002832.dat"/>
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73 <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
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74 </test>
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75
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76 </tests>
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77
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2
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78 <help>
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79 Convert mascot results from mascotdat to pepXML
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80 </help>
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81
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82 </tool>
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