<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
	<requirements>
	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
   </requirements>

  <description>Converts a mascot results file to pepXML</description>

<command>rvm 1.9.3@protk-1.2.2 do 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>