Mercurial > repos > da-intersect > ap11_test

diff protein_merger.xml @ 5:795f289b64db draft

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First complete upload, containing the datatype TAR.
author da-intersect
date Wed, 10 Apr 2013 02:41:02 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_merger.xml	Wed Apr 10 02:41:02 2013 -0400
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+<tool id="protmerger" name="Protein Merger" version="0.0.1">
+        <description>Virtual Protein Merger</description>
+        <command interpreter="bash">
+        protein_merger.sh virtual_protein_merger.jar -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>