# HG changeset patch
# User peterjc
# Date 1336581606 14400
# Node ID 216bf640baaf00502d7bfb56df32d5431e05d839
# Parent  117cce3296afad460dfe201092298db5667970d2
Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.

diff -r 117cce3296af -r 216bf640baaf tools/sr_assembly/mira.txt
--- a/tools/sr_assembly/mira.txt	Wed Dec 21 11:33:19 2011 -0500
+++ b/tools/sr_assembly/mira.txt	Wed May 09 12:40:06 2012 -0400
@@ -36,10 +36,11 @@
 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
-         (some other switched changed, e.g. -OUT rrol to rrot, which
+         (some other switches changed, e.g. -OUT rrol to rrot, which
          means the wrapper no longer works with MIRA 3.2.x)
        - The contig summary file (TCS file) was removed in MIRA 3.4
        - Report all missing output files (not just first missing one)
+v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
 
 
 Developers
diff -r 117cce3296af -r 216bf640baaf tools/sr_assembly/mira.xml
--- a/tools/sr_assembly/mira.xml	Wed Dec 21 11:33:19 2011 -0500
+++ b/tools/sr_assembly/mira.xml	Wed May 09 12:40:06 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3">
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.4">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
 	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
 ##Give the wrapper script list of output filenames, then the mira command...
@@ -7,7 +7,7 @@
 ##Input files
 #if $condBackbone.use == "true":
     ## Can this be linked to job_method as well? If mapping we need the backbone...
-    -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename}
+    -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
 #end if
 #if $condSanger.use == "true":
     SANGER_SETTINGS