# HG changeset patch # User peterjc # Date 1384533894 18000 # Node ID 6e145e4715a7e9ed2afc2a15e8af834b824b936d # Parent 6c899e228df3b9fb427cd766b363ca40418320b3 Uploaded v0.0.1b diff -r 6c899e228df3 -r 6e145e4715a7 tools/clc_assembly_cell/clc_assembler.xml --- a/tools/clc_assembly_cell/clc_assembler.xml Thu Oct 31 07:59:32 2013 -0400 +++ b/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 15 11:44:54 2013 -0500 @@ -23,6 +23,7 @@ #end if ##-------------------------------------- #end for +-m $min_contig_len -o "$out_fasta" --cpus \$GALAXY_SLOTS -v | grep -v "^Progress: " @@ -86,10 +87,10 @@ + - @@ -97,7 +98,19 @@ - + diff -r 6c899e228df3 -r 6e145e4715a7 tools/clc_assembly_cell/clc_mapper.xml --- a/tools/clc_assembly_cell/clc_mapper.xml Thu Oct 31 07:59:32 2013 -0400 +++ b/tools/clc_assembly_cell/clc_mapper.xml Fri Nov 15 11:44:54 2013 -0500 @@ -10,7 +10,7 @@ echo Mapping reads with clc_mapper... && /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_mapper #for $ref in $references -#if str($ref.type)=="circular" +#if str($ref.ref_type)=="circular" -d -z "$ref.ref_file" #else -d "$ref.ref_file" @@ -61,11 +61,11 @@ - + - + @@ -125,13 +125,26 @@ - + - +