<tool id="resanalyser" name="Result Analyser" version="1.0.8">
        <description>Result Analyser</description>
        <command interpreter="bash">
        result_analyser.sh results_analyser.jar $chromosome_tar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" 
        #if $reportId
        -rep "$reportId"
        #end if
        #if $reportList
        -replist "$reportList"
        #end if
        #if $sqlQuery
        -sql "$sqlQuery"
        #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="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />

		<param name="reportId" optional="true" type="data" format="txt" label="Select reportId" help="Access a built in report query" />
		<param name="reportList" optional="true" type="data" format="txt" label="Select reportList" help="A file containing all the pre-built SQL queries" />
		<param name="sqlQuery" optional="true" type="data" format="txt" label="Select SQL Query" help="Filters the result through the use of a SQL statement to the output file" />

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