view protein_merger.xml @ 3:0b76c960dd38 draft

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<tool id="protmerger" name="Protein Merger" version="0.0.1">
        <description>Virtual Protein Merger</description>
        <command interpreter="bash">
        javaRunner.sh virtual_protein_merger.jar -c "/usr/local/galaxy-dist/tools/ap11/chromosome/" -g "$genomeFile" -o "$output1" 
        -r "$searchResultsFile" 
	#if $trans_tab_file
	-t "$trans_tab_file"
	#end if
        </command>
        <inputs>
        	<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"/>

	</inputs>
        <outputs>
                <data format="sam" name="output1" />
        </outputs>
        <help>
        </help>
</tool>