# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1275657576 14400 # Node ID f0c8355714e2b1fc1f70026485a4b24843609b2a # Parent e924fd0ed0174300161577c30936c649d2cd2d08 Update cufflinks wrapper and tests. Expression output files are now tabular and all outputs are evaluated in functional test.

--- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -50,12 +50,15 @@ </inputs><outputs> - <data format="expr" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> - <data format="expr" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/> + <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> + <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/></outputs><tests> + <!-- + Simple test that uses test data included with cufflinks. + --><test><param name="sPaired" value="single"/><param name="input" value="cufflinks_in.sam"/> @@ -65,12 +68,9 @@ <param name="pre_mrna_fraction" value="0.05"/><param name="min_map_quality" value="0"/><param name="use_ref" value="No"/> - <output name="assembled_isoforms" file="cufflinks_out1.gtf"/> - <!-- - Can't test these right now b/c .expr files aren't recognized. Need to add them? <output name="genes_expression" format="tabular" file="cufflinks_out3.expr"/><output name="transcripts_expression" format="tabular" file="cufflinks_out2.expr"/> - --> + <output name="assembled_isoforms" file="cufflinks_out1.gtf"/></test></tests>