# 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 @@
-
+
-
+