Mercurial > repos > iracooke > mascot

annotate mascot_to_pepxml.xml @ 10:b3427b77073e draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:50:46 -0400
parents f567d1818b84
children
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b3427b77073e planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1">
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iracooke
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2 <description>Converts a mascot results file to pepXML</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.3</container>
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5 <requirement type="package" version="1.4.3">protk</requirement>
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6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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7 </requirements>
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8 <command>mascot_to_pepxml.rb
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9 $input_file
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11 -o $output
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13 #if $database.source_select=="built_in":
b3427b77073e planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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14 -d $database.dbkey
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15 #else
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16 -d $database.fasta_file
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17 #end if
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18
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19 #if $explicit_enzyme.explicit_enzyme_use
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20 --enzyme $explicit_enzyme.enzyme
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21 #end if
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23 $shortid
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24 </command>
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25 <inputs>
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26 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
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28 <conditional name="database">
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29 <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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iracooke
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30 <option value="built_in">Built-In</option>
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31 <option value="input_ref">Uploaded fasta file</option>
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32 </param>
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33 <when value="built_in">
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34 <param name="dbkey" type="select" format="text" >
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35 <label>Database</label>
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36 <options from_file="pepxml_databases.loc">
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37 <column name="name" index="0" />
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38 <column name="value" index="2" />
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39 </options>
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40 </param>
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41 </when>
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42 <when value="input_ref">
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43 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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44 </when>
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45 </conditional>
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46
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47 <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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49 <conditional name="explicit_enzyme">
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50 <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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51 <when value="false" />
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52 <when value="true">
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53 <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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54 </when>
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55 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="source_select" value="input_ref"/>
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64 <param name="fasta_file" value="bsa.fasta"/>
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65 <param name="input_file" value="F002832.dat"/>
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66 <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
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67 </test>
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68 </tests>
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69 <help>
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70 Convert mascot results from mascotdat to pepXML
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71 </help>
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72 </tool>