1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36c540d788c3/ changeset: 36c540d788c3 user: jgoecks date: 2012-06-11 21:52:36 summary: Have Bowtie2 wrapper produce BAM rather than SAM output. affected #: 2 files diff -r 17302ca3be4e7b3d987733ea6e61982f9520996d -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -65,7 +65,7 @@ index_path = options.index_path # Build bowtie command. - cmd = 'bowtie2 %s -x %s %s -S %s' + cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s' # Set up reads. if options.single_paired == 'paired': diff -r 17302ca3be4e7b3d987733ea6e61982f9520996d -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -112,7 +112,7 @@ </inputs><outputs> - <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.