1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20e2d056b843/ Changeset: 20e2d056b843 User: jgoecks Date: 2013-08-05 23:08:28 Summary: Tophat2 wrapper enhancements: (a) better error handling; (b) include alignment statistics in output; and (c) document compatible tool versions. Affected #: 1 file diff -r af1daa86ba5b713240fb3f7ccd607f3adb8c05a7 -r 20e2d056b843504ea77c49adc0cb08818bb7bdc6 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -1,5 +1,5 @@ -<tool id="tophat2" name="Tophat2" version="0.5"> - <!-- Wrapper compatible with Tophat version 2.0.0 --> +<tool id="tophat2" name="Tophat2" version="0.6"> + <!-- Wrapper compatible with Tophat version 2.0.0+ --><description>Gapped-read mapper for RNA-seq data</description><version_command>tophat2 --version</version_command><requirements> @@ -268,11 +268,12 @@ </inputs><stdio> - <regex match="Exception" source="both" level="fatal" description="Tool exception"/> + <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/><regex match=".*" source="both" level="log" description="tool progress"/></stdio><outputs> + <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/><data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"><filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data> @@ -312,6 +313,7 @@ </actions></macro></macros> + <tests><!-- Test base-space single-end reads with pre-built index and preset parameters --><test> 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.