# HG changeset patch
# User geert-vandeweyer
# Date 1406898487 14400
# Node ID e87fb5178f4bd758a6c51ab6ebde70a05e91f720
# Parent  82f0d5660884330282dc9f129fed0eaf3244a9d2
correction to conditional variables

diff -r 82f0d5660884 -r e87fb5178f4b cufflinks_wrapper.xml
--- a/cufflinks_wrapper.xml	Fri Aug 01 08:58:06 2014 -0400
+++ b/cufflinks_wrapper.xml	Fri Aug 01 09:08:07 2014 -0400
@@ -18,13 +18,13 @@
             ## Include reference annotation?
             #if $reference_annotation.use_ref == "Use reference annotation":
                 -G $reference_annotation.reference_annotation_file
-		$compatible_hits_norm
+		$reference_annoation.compatible_hits_norm
             #end if
             #if $reference_annotation.use_ref == "Use reference annotation guide":
 		        -g $reference_annotation.reference_annotation_guide_file
-			--3-overhang-tolerance=$3_overhang_tolerance
-			--intron-overhang-tolerance=$intron_overhang_tolerance
-			$no_faux_reads
+			--3-overhang-tolerance=$reference_annotation.3_overhang_tolerance
+			--intron-overhang-tolerance=$reference_annotation.intron_overhang_tolerance
+			$reference_annotation.no_faux_reads
             #end if
 
             ## Bias correction?
@@ -189,7 +189,7 @@
         <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
         <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
         <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
-	<data format="gtf" name="skipped.gtf" lable="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/>
+	<data format="gtf" name="skipped.gtf" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/>
     </outputs>
 
     <trackster_conf>