# HG changeset patch
# User geert-vandeweyer
# Date 1406898907 14400
# Node ID e5139e144b567fd77116eadd3f06df12a30d2ad6
# Parent  065e8d11a08c6e6d7933e1a970bc937200cf5593
3_xxx format in paramater naming is illegal.

diff -r 065e8d11a08c -r e5139e144b56 cufflinks_wrapper.xml
--- a/cufflinks_wrapper.xml	Fri Aug 01 09:09:55 2014 -0400
+++ b/cufflinks_wrapper.xml	Fri Aug 01 09:15:07 2014 -0400
@@ -22,7 +22,7 @@
             #end if
             #if $reference_annotation.use_ref == "Use reference annotation guide":
 		        -g $reference_annotation.reference_annotation_guide_file
-			--3-overhang-tolerance=$reference_annotation.3_overhang_tolerance
+			--3-overhang-tolerance=$reference_annotation.three_overhang_tolerance
 			--intron-overhang-tolerance=$reference_annotation.intron_overhang_tolerance
 			$reference_annotation.no_faux_reads
             #end if
@@ -62,8 +62,8 @@
 		--max-bundle-length=$advanced_settings.max_bundle_length
 		--max-bundle-frags=$advanced_settings.max_bundle_frags
 		--min-intron-length=$advanced_settings.min_intron_length
-		--trim-3-avgcov-thresh=$advanced_settings.trim_3_avgcov_thresh
-		--trim-3-dropoff-frac=$advanced_settings.trim_3_dropoff_frac
+		--trim-3-avgcov-thresh=$advanced_settings.trim_three_avgcov_thresh
+		--trim-3-dropoff-frac=$advanced_settings.trim_three_dropoff_frac
 	    #end if
 
     </command>
@@ -88,7 +88,7 @@
             </when>
             <when value="Use reference annotation guide">
                 <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
-		<param name="3_overhang_tolerance" type="integer" value="600" label="3prime 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." />
+		<param name="three_overhang_tolerance" type="integer" value="600" label="3prime 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." />
 		<param name="intron_overhang_tolerance" type="integer" value="50" label="Intronic 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." />
 		<param name="no_faux_reads" type="select" label="Disable tiling of reference transcripts" help="This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.">
 			<option value="" selected="True">No</option>
@@ -176,9 +176,9 @@
 
 		<param name="min_intron_length" type="integer" value="50" label="Minimal allowed intron size" help="Default: 50bp" />
 
-		<param name="trim_3_avgcov_thresh" type="integer" value="10" label="Minimum average coverage required to attempt 3prime trimming." help="Default: 10" />
+		<param name="trim_three_avgcov_thresh" type="integer" value="10" label="Minimum average coverage required to attempt 3prime trimming." help="Default: 10" />
 		
-		<param name="trim_3_dropoff_frac" type="float" value="0.1" min="0" max="1" label="The fraction of average coverage below which to trim the 3prime end of an assembled transcript." help="Default: 0.1"/>
+		<param name="trim_three_dropoff_frac" type="float" value="0.1" min="0" max="1" label="The fraction of average coverage below which to trim the 3prime end of an assembled transcript." help="Default: 0.1"/>
 
 	    </when>
 	</conditional>