1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7446b7287335/ changeset: 7446b7287335 user: jgoecks date: 2012-04-18 15:23:33 summary: Tophat wrapper: (a) add documentation for versions supported and (b) always return insertions and deletetions outputs. affected #: 1 file diff -r c995f2ffa59c4803f960ef14742119e7bf477757 -r 7446b72873356baaa9c7ec60dd7e8bb0a34fe4d7 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,4 +1,5 @@ -<tool id="tophat" name="Tophat for Illumina" version="1.5.0"> +<tool id="tophat" name="Tophat for Illumina" version="0.5"> + <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 --><description>Find splice junctions using RNA-seq data</description><version_command>tophat --version</version_command><requirements> @@ -386,14 +387,6 @@ <outputs><data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> - <filter> - ( - ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and - ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or - ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and - ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) - ) - </filter><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -413,14 +406,6 @@ </actions></data><data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> - <filter> - ( - ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and - ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or - ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and - ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) - ) - </filter><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.