# HG changeset patch
# User iuc
# Date 1468839004 14400
# Node ID e3f369973054de9e811d2a943c66048fcc46e397
# Parent  d0bb240d7525add8d8c05f56075020bf6d9e3545
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0

diff -r d0bb240d7525 -r e3f369973054 stringtie.xml
--- a/stringtie.xml	Wed Jul 13 14:48:26 2016 -0400
+++ b/stringtie.xml	Mon Jul 18 06:50:04 2016 -0400
@@ -79,25 +79,25 @@
     <outputs>
         <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
         <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
-            <filter>option_set['abundance_estimation']</filter>
+            <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
         </data>
         <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
-            <filter>guide['use_guide'] == "yes"</filter>
+            <filter>guide['use_guide'] == 'yes'</filter>
         </data>
         <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
-            <filter>guide['output_ballgown']</filter>
+            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
         </data>
         <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
-            <filter>guide['output_ballgown']</filter>
+            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
         </data>
         <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
-            <filter>guide['output_ballgown']</filter>
+            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
         </data>
         <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
-            <filter>guide['output_ballgown']</filter>
+            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
         </data>
         <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
-            <filter>guide['output_ballgown']</filter>
+            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
         </data>
     </outputs>
     <tests>
@@ -204,4 +204,3 @@
     </help>
     <expand macro="citations" />
 </tool>
-    
\ No newline at end of file