1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1df26d9240bb/ changeset: 1df26d9240bb user: jgoecks date: 2012-06-11 14:49:31 summary: Handle Tophat2 fusion-ignore-chromosome parameter correctly. affected #: 2 files
diff -r 0edd1d65d746a806de155d3d37428ac84b4265ff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -200,10 +200,12 @@
# Fusion search options. if options.fusion_search: - opts += ' --fusion-search --fusion-anchor-length %i --fusion-min-dist %i --fusion-read-mismatches %i --fusion-multireads %i --fusion-multipairs %i --fusion-ignore-chromosomes %s' % \ + opts += ' --fusion-search --fusion-anchor-length %i --fusion-min-dist %i --fusion-read-mismatches %i --fusion-multireads %i --fusion-multipairs %i' % \ ( int( options.fusion_anchor_length ), int( options.fusion_min_dist ), int( options.fusion_read_mismatches ), int( options.fusion_multireads ), - int( options.fusion_multipairs ), options.fusion_ignore_chromosomes ) + int( options.fusion_multipairs ) ) + if options.fusion_ignore_chromosomes: + opts += ' --fusion-ignore-chromosomes %s' % options.fusion_ignore_chromosomes
# Bowtie2 options. if options.b2_very_fast:
diff -r 0edd1d65d746a806de155d3d37428ac84b4265ff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -103,7 +103,7 @@ --fusion-read-mismatches $params.fusion_search.read_mismatches --fusion-multireads $params.fusion_search.multireads --fusion-multipairs $params.fusion_search.multipairs - --fusion-ignore-chromosomes $params.fusion_search.ignore_chromosomes + --fusion-ignore-chromosomes "$params.fusion_search.ignore_chromosomes" #end if
#if $params.bowtie2_settings.b2_settings == "Yes":
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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