# HG changeset patch --
Bitbucket.org
# Project galaxy-dist
# URL
http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)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>