Mercurial > repos > iracooke > mascot
diff mascot_to_pepxml.xml @ 10:b3427b77073e draft default tip
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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--- a/mascot_to_pepxml.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot_to_pepxml.xml Tue Oct 20 19:50:46 2015 -0400 @@ -1,83 +1,72 @@ -<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> +<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1"> + <description>Converts a mascot results file to pepXML</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command>mascot_to_pepxml.rb + $input_file - <description>Converts a mascot results file to pepXML</description> - -<command>mascot_to_pepxml.rb - $input_file - - -o $output + -o $output - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if + #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 + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if -</command> -<inputs> - - - <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> + $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> + <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="" /> + <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> + <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> - <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> - + </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>