Mercurial > repos > iracooke > mascot
comparison mascot_to_pepxml.xml @ 7:75184e45bf84 draft
Uploaded
| author | iracooke |
|---|---|
| date | Fri, 13 Jun 2014 18:26:31 -0400 |
| parents | |
| children | f567d1818b84 |
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| 6:f36b84d1ac09 | 7:75184e45bf84 |
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| 1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.2"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.3">protk</requirement> | |
| 4 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <description>Converts a mascot results file to pepXML</description> | |
| 8 | |
| 9 <command>mascot_to_pepxml.rb | |
| 10 $input_file | |
| 11 | |
| 12 -o $output | |
| 13 | |
| 14 #if $database.source_select=="built_in": | |
| 15 -d $database.dbkey | |
| 16 #else | |
| 17 -d $database.fasta_file | |
| 18 #end if | |
| 19 | |
| 20 #if $explicit_enzyme.explicit_enzyme_use | |
| 21 --enzyme $explicit_enzyme.enzyme | |
| 22 #end if | |
| 23 | |
| 24 $shortid | |
| 25 | |
| 26 </command> | |
| 27 <inputs> | |
| 28 | |
| 29 | |
| 30 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> | |
| 31 | |
| 32 <conditional name="database"> | |
| 33 <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search"> | |
| 34 <option value="built_in">Built-In</option> | |
| 35 <option value="input_ref">Uploaded fasta file</option> | |
| 36 </param> | |
| 37 <when value="built_in"> | |
| 38 <param name="dbkey" type="select" format="text" > | |
| 39 <label>Database</label> | |
| 40 <options from_file="pepxml_databases.loc"> | |
| 41 <column name="name" index="0" /> | |
| 42 <column name="value" index="2" /> | |
| 43 </options> | |
| 44 </param> | |
| 45 </when> | |
| 46 <when value="input_ref"> | |
| 47 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 | |
| 51 <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" /> | |
| 52 | |
| 53 <conditional name="explicit_enzyme"> | |
| 54 <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" /> | |
| 55 <when value="false" /> | |
| 56 <when value="true"> | |
| 57 <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/> | |
| 58 </when> | |
| 59 </conditional> | |
| 60 | |
| 61 | |
| 62 | |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> | |
| 66 </outputs> | |
| 67 | |
| 68 <tests> | |
| 69 <test> | |
| 70 <param name="source_select" value="input_ref"/> | |
| 71 <param name="fasta_file" value="bsa.fasta"/> | |
| 72 <param name="input_file" value="F002832.dat"/> | |
| 73 <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> | |
| 74 </test> | |
| 75 | |
| 76 </tests> | |
| 77 | |
| 78 <help> | |
| 79 Convert mascot results from mascotdat to pepXML | |
| 80 </help> | |
| 81 | |
| 82 </tool> |