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Complete functional test for cuffcompare.

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This commit is contained in:
Jeremy Goecks
2010-10-26 15:04:41 -04:00
parent 7fd09cf4a8
commit d75830965b
1 changed files with 5 additions and 6 deletions
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tools/ngs_rna/cuffcompare_wrapper.xml
+5 -6
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@@ -81,16 +81,15 @@
<param name="use_ref_annotation" value="Yes"/>
<param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
<param name="ignore_nonoverlapping_reference" value="Yes"/>
## HACK: need to specify output name and it needs to work (right now it uses the final output file)
<output name="XXXX" file="cuffcompare_out6.tracking"/>
<!--
## TODO: transcripts combined file as well.
<!-- Line diffs are the result of different locations for input files; this cannot be fixed as cuffcompare outputs
full input path for each input. -->
<output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/>
<output name="input1_tmap" file="cuffcompare_out1.tmap"/>
<output name="input1_refmap" file="cuffcompare_out2.refmap"/>
<output name="input2_tmap" file="cuffcompare_out3.tmap"/>
<output name="input2_refmap" file="cuffcompare_out4.refmap"/>
<output name="transcripts_accuracy" file="cuffcompare_out7.txt"/>
-->
<output name="transcripts_combined" file="cuffcompare_out5.gtf"/>
<output name="transcripts_tracking" file="cuffcompare_out6.tracking"/>
</test>
</tests>