--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/result_analyser.xml	Thu Jun 27 20:38:20 2013 -0400
@@ -0,0 +1,31 @@
+<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>