# HG changeset patch
# User da-intersect
# Date 1366350672 14400
# Node ID e9aa05006fa7e6568eae2b5d2b6797366ebfcc61
# Parent  1847c7a8492ed30a846919c347917816cf17888d
Change to virtual_protein_merger

diff -r 1847c7a8492e -r e9aa05006fa7 datatypes_conf.xml
diff -r 1847c7a8492e -r e9aa05006fa7 jars/virtual_protein_merger.jar
Binary file jars/virtual_protein_merger.jar has changed
diff -r 1847c7a8492e -r e9aa05006fa7 protein_generator.xml
diff -r 1847c7a8492e -r e9aa05006fa7 protein_merger.xml
--- a/protein_merger.xml	Sun Apr 14 18:57:15 2013 -0400
+++ b/protein_merger.xml	Fri Apr 19 01:51:12 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="protmerger" name="Protein Merger" version="1.0.1">
+<tool id="protmerger" name="Protein Merger" version="1.0.2">
         <description>Virtual Protein Merger</description>
         <command interpreter="bash">
         protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1" 
@@ -6,13 +6,16 @@
 	#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" />
diff -r 1847c7a8492e -r e9aa05006fa7 result_analyser.xml
diff -r 1847c7a8492e -r e9aa05006fa7 tar.py