# HG changeset patch
# User bcrain-completegenomics
# Date 1339521966 14400
# Node ID 63541ee5f3192d63f0fddd22c4f65c459f7a2663
# Parent ed3c76be8a416dd3be34f78f53a0385043d462e5
Uploaded
diff -r ed3c76be8a41 -r 63541ee5f319 cgatools/tools/cgatools/junctiondiff.xml
--- a/cgatools/tools/cgatools/junctiondiff.xml Tue Jun 12 13:25:24 2012 -0400
+++ b/cgatools/tools/cgatools/junctiondiff.xml Tue Jun 12 13:26:06 2012 -0400
@@ -7,16 +7,74 @@
- cgatools junctiondiff --beta -h
+ cgatools junctiondiff --beta
+ --reference $crr.fields.path
+ --junctionsA $data_sources.inputA
+ --junctionsB $data_sources.inputB
+ --scoreThresholdA $scoreA
+ --scoreThresholdB $scoreB
+ --distance $distance
+ --minlength $minlength
+ $stat
+ --output-prefix cg_
+ ;
+ mv cg_diff-*tsv cg_diff.tsv
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+ (stat == '--statout')
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**What it does**