# HG changeset patch
# User devteam
# Date 1428598361 14400
# Node ID 64698e16f4a68c8f847e093d3fa18d3460e8c6d2
# Parent  5346d5eea8b1bd3fd91afa761a0f70304e94a134
Uploaded

diff -r 5346d5eea8b1 -r 64698e16f4a6 cufflinks_wrapper.py
--- a/cufflinks_wrapper.py	Fri Dec 19 11:58:22 2014 -0500
+++ b/cufflinks_wrapper.py	Thu Apr 09 12:52:41 2015 -0400
@@ -17,7 +17,7 @@
     parser.add_option( '-j', '--pre-mrna-fraction', dest='pre_mrna_fraction', help='Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.' )
     parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
     parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' )
-    parser.add_option ("--compatible-hits-norm",dest='compatible_hits_norm',help='Count hits compatible with reference RNAs only')
+    parser.add_option("--compatible-hits-norm", dest='compatible_hits_norm', action="store_true", help='Count hits compatible with reference RNAs only')
     parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' )
     parser.add_option("--3-overhang-tolerance",dest='three_overhang_tolerance', help='The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp.')
     parser.add_option("--intron-overhang-tolerance",dest='intron_overhang_tolerance',help='The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp.')