# HG changeset patch
# User edward-kirton
# Date 1307483464 14400
# Node ID 368a6ebebddeb275a9a88b192cac9176cd102e59
# Parent  f036c7107601f5baf299287ae12b2cb3e8c4ca24
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

diff -r f036c7107601 -r 368a6ebebdde roche454/runMapping.xml
--- a/roche454/runMapping.xml	Tue Jun 07 17:50:32 2011 -0400
+++ b/roche454/runMapping.xml	Tue Jun 07 17:51:04 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="runMapping" name="runMapping" version="1.0.0">
+<tool id="runMapping" name="runMapping" version="1.0.1">
 <description>Map Roche/454 reads to a reference using Newbler</description>
 <command interpreter='perl'>runMapping_wrapper.pl
 $newbler_metrics.extra_files_path
diff -r f036c7107601 -r 368a6ebebdde roche454/runMapping_cDNA.xml
--- a/roche454/runMapping_cDNA.xml	Tue Jun 07 17:50:32 2011 -0400
+++ b/roche454/runMapping_cDNA.xml	Tue Jun 07 17:51:04 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.0">
+<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.1">
 <description>Map Roche/454 reads to a reference using Newbler</description>
 <command interpreter='perl'>runMapping_cDNA_wrapper.pl
 $newbler_metrics.extra_files_path
diff -r f036c7107601 -r 368a6ebebdde roche454/runMapping_cDNA_wrapper.pl
--- a/roche454/runMapping_cDNA_wrapper.pl	Tue Jun 07 17:50:32 2011 -0400
+++ b/roche454/runMapping_cDNA_wrapper.pl	Tue Jun 07 17:51:04 2011 -0400
@@ -9,11 +9,11 @@
 my $alignment_info=shift @ARGV;
 my $all_contigs_fasta=shift @ARGV;
 my $all_contigs_qual=shift @ARGV;
-my $all_diffs=shift @ARGV
-my $all_struct_vars=shift @ARGV
-my $hc_diff=shift @ARGV
-my $hc_struct_vars=shift @ARGV
-my $mapping_qc=shift @ARGV
+my $all_diffs=shift @ARGV;
+my $all_struct_vars=shift @ARGV;
+my $hc_diff=shift @ARGV;
+my $hc_struct_vars=shift @ARGV;
+my $mapping_qc=shift @ARGV;
 my $newbler_metrics=shift @ARGV;
 my $pair_align=shift @ARGV;
 my $read_status=shift @ARGV;
diff -r f036c7107601 -r 368a6ebebdde roche454/runMapping_wrapper.pl
--- a/roche454/runMapping_wrapper.pl	Tue Jun 07 17:50:32 2011 -0400
+++ b/roche454/runMapping_wrapper.pl	Tue Jun 07 17:51:04 2011 -0400
@@ -8,11 +8,11 @@
 my $alignment_info=shift @ARGV;
 my $all_contigs_fasta=shift @ARGV;
 my $all_contigs_qual=shift @ARGV;
-my $all_diffs=shift @ARGV
-my $all_struct_vars=shift @ARGV
-my $hc_diff=shift @ARGV
-my $hc_struct_vars=shift @ARGV
-my $mapping_qc=shift @ARGV
+my $all_diffs=shift @ARGV;
+my $all_struct_vars=shift @ARGV;
+my $hc_diff=shift @ARGV;
+my $hc_struct_vars=shift @ARGV;
+my $mapping_qc=shift @ARGV;
 my $newbler_metrics=shift @ARGV;
 my $pair_align=shift @ARGV;
 my $read_status=shift @ARGV;
diff -r f036c7107601 -r 368a6ebebdde roche454/suite_config.xml
--- a/roche454/suite_config.xml	Tue Jun 07 17:50:32 2011 -0400
+++ b/roche454/suite_config.xml	Tue Jun 07 17:51:04 2011 -0400
@@ -1,4 +1,4 @@
-<suite id="roche454_toolsuite" name="Suite of Newbler tools" version="1.0.0">
+<suite id="roche454_toolsuite" name="Suite of Newbler tools" version="1.0.1">
 	<description>This suite contains Roche/454's Newbler and sff-fastq converter</description>
 	<tool id="runAssembly" name="runAssembly" version="1.0.0">
 		<description>Assemble 454 gDNA reads</description>
@@ -6,10 +6,10 @@
 	<tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.0">
 		<description>Assemble 454 cDNA reads</description>
 	</tool>
-	<tool id="runMapping" name="runMapping" version="1.0.0">
+	<tool id="runMapping" name="runMapping" version="1.0.1">
 		<description>Map 454 cDNA reads to reference</description>
 	</tool>
-	<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.0">
+	<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.1">
 		<description>Map 454 cDNA reads to reference</description>
 	</tool>
 	<tool id="sff_to_fastq" name="Sff to Fastq Converter" version="1.0.0">