Mercurial > repos > iracooke > mascot
diff mascot_to_pepxml.xml @ 7:75184e45bf84 draft
Uploaded
author | iracooke |
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date | Fri, 13 Jun 2014 18:26:31 -0400 |
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children | f567d1818b84 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mascot_to_pepxml.xml Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,82 @@ +<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.2"> + <requirements> + <requirement type="package" version="1.3">protk</requirement> + <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> + </requirements> + + <description>Converts a mascot results file to pepXML</description> + +<command>mascot_to_pepxml.rb + $input_file + + -o $output + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if + + $shortid + +</command> +<inputs> + + + <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> + + <conditional name="database"> + <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search"> + <option value="built_in">Built-In</option> + <option value="input_ref">Uploaded fasta file</option> + </param> + <when value="built_in"> + <param name="dbkey" type="select" format="text" > + <label>Database</label> + <options from_file="pepxml_databases.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + </when> + <when value="input_ref"> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + </when> + </conditional> + + <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" /> + + <conditional name="explicit_enzyme"> + <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/> + </when> + </conditional> + + + +</inputs> +<outputs> + <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> +</outputs> + + <tests> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="bsa.fasta"/> + <param name="input_file" value="F002832.dat"/> + <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> + </test> + + </tests> + +<help> + Convert mascot results from mascotdat to pepXML +</help> + +</tool>