<tool id="protmerger" name="Protein Merger" version="1.0.9">
        <description>Virtual Protein Merger</description>
        <command interpreter="bash">
        protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1" 
        -r "$searchResultsFile" 
	#if $trans_tab_file
	-t "$trans_tab_file"
	#end if
	#if $confidence_score
	-s "$confidence_score"
	#end if
        </command>
        <inputs>
        	<param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
        	<param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
        	<param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
		<param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="True"/>
		<param name="confidence_score" type="integer" label="Confidence score thresold" help="Minimum confidence score for peptides to be included" optional="True" />
	</inputs>
        <outputs>
                <data format="sam" name="output1" />
        </outputs>
        <help>
        </help>
</tool>