--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/protein_merger.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,25 @@
+<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>