# HG changeset patch
# User da-intersect
# Date 1365639323 -36000
# Node ID eb1e67dae7b6dce1e9b71452ca8de9c6dabc1b2e
# Parent  956779875d035331fe5d5bed62757ea40389476e
Updated all config and scripts

diff -r 956779875d03 -r eb1e67dae7b6 protein_merger.xml
--- a/protein_merger.xml	Wed Apr 10 03:13:51 2013 -0400
+++ b/protein_merger.xml	Thu Apr 11 10:15:23 2013 +1000
@@ -1,17 +1,17 @@
 <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" 
+        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
         </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"/>
-
 	</inputs>
         <outputs>
                 <data format="sam" name="output1" />
diff -r 956779875d03 -r eb1e67dae7b6 result_analyser.xml
--- a/result_analyser.xml	Wed Apr 10 03:13:51 2013 -0400
+++ b/result_analyser.xml	Thu Apr 11 10:15:23 2013 +1000
@@ -1,7 +1,7 @@
 <tool id="resanalyser" name="Result Analyser" version="0.0.1">
         <description>Result Analyser</description>
         <command interpreter="bash">
-        result_analyser.sh results_analyser.jar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" 
+        result_analyser.sh results_analyser.jar $chromosome_tar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" 
         #if $reportId
         -rep "$reportId"
         #end if
@@ -13,6 +13,7 @@
         #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" />
diff -r 956779875d03 -r eb1e67dae7b6 samifier.xml
--- a/samifier.xml	Wed Apr 10 03:13:51 2013 -0400
+++ b/samifier.xml	Thu Apr 11 10:15:23 2013 +1000
@@ -13,7 +13,7 @@
 	#end if
         </command>
         <inputs>
-        	<param name="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" />
+        	<param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
         	<param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
         	<param name="mascot" 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" />