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Setup for cuffdiff functional test.

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This commit is contained in:
Jeremy Goecks
2010-05-26 16:47:11 -04:00
parent 109cbee000
commit aa87decb0b
1 changed files with 17 additions and 1 deletions
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tools/ngs_rna/cuffdiff_wrapper.xml
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@@ -59,6 +59,22 @@
<tests>
<test>
<!--
cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
-->
<param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
<param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
<param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
<!-- Defaults. -->
<param name="fdr" value="0.05" />
<param name="min_mapqual" value="0" ftype="sam" />
<param name="min_alignment_count" value="0" ftype="sam" />
<param name="sPaired" value="single" ftype="sam" />
<!-- This won't pass until the test harness is updated to handle outputs better. -->
<!--
<output name="XXXX" file="cuffdiff_out5.tracking" />
-->
</test>
</tests>
@@ -83,7 +99,7 @@ There is no such thing (yet) as an automated gearshift in expression analysis. I
**Input format**
Cuffcompare takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
.. ___: http://www.todo.org