# HG changeset patch # User edward-kirton # Date 1307481819 14400 # Node ID 584549c024c25b76f56007960de7f3a30e030907 # Parent 9e30cc10a6a3f9ec0eeae73801cee025539f9a76 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository diff -r 9e30cc10a6a3 -r 584549c024c2 roche454/runMapping.xml --- a/roche454/runMapping.xml Tue Jun 07 17:23:05 2011 -0400 +++ b/roche454/runMapping.xml Tue Jun 07 17:23:39 2011 -0400 @@ -1,4 +1,4 @@ - + Map Roche/454 reads to a reference using Newbler runMapping_wrapper.pl $newbler_metrics.extra_files_path diff -r 9e30cc10a6a3 -r 584549c024c2 roche454/runMapping_cDNA.xml --- a/roche454/runMapping_cDNA.xml Tue Jun 07 17:23:05 2011 -0400 +++ b/roche454/runMapping_cDNA.xml Tue Jun 07 17:23:39 2011 -0400 @@ -1,4 +1,4 @@ - + Map Roche/454 reads to a reference using Newbler runMapping_cDNA_wrapper.pl $newbler_metrics.extra_files_path diff -r 9e30cc10a6a3 -r 584549c024c2 roche454/runMapping_cDNA_wrapper.pl --- a/roche454/runMapping_cDNA_wrapper.pl Tue Jun 07 17:23:05 2011 -0400 +++ b/roche454/runMapping_cDNA_wrapper.pl Tue Jun 07 17:23:39 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 9e30cc10a6a3 -r 584549c024c2 roche454/runMapping_wrapper.pl --- a/roche454/runMapping_wrapper.pl Tue Jun 07 17:23:05 2011 -0400 +++ b/roche454/runMapping_wrapper.pl Tue Jun 07 17:23:39 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 9e30cc10a6a3 -r 584549c024c2 roche454/suite_config.xml --- a/roche454/suite_config.xml Tue Jun 07 17:23:05 2011 -0400 +++ b/roche454/suite_config.xml Tue Jun 07 17:23:39 2011 -0400 @@ -1,4 +1,4 @@ - + This suite contains Roche/454's Newbler and sff-fastq converter Assemble 454 gDNA reads @@ -6,10 +6,10 @@ Assemble 454 cDNA reads - + Map 454 cDNA reads to reference - + Map 454 cDNA reads to reference