# HG changeset patch
# User greg
# Date 1483555929 18000
# Node ID b75510484c1605069f700162471c75eb113e831a
# Parent  b0a29067fc353a40de0c639de3b220dfd4655404
Uploaded

diff -r b0a29067fc35 -r b75510484c16 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Jan 04 13:38:07 2017 -0500
+++ b/gene_family_classifier.xml	Wed Jan 04 13:52:09 2017 -0500
@@ -37,9 +37,13 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
+            #if str($classifier) == 'hmmscan' or str($classifier) == 'both':
+                # Eliminate the hmmscan.log file
+                && rm $src_dir/*.log
+            #end if
             #if create_ortho_sequences:
-                echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output &&
-                mv $src_dir/* $dest_dir
+                && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output
+                && mv $src_dir/* $dest_dir
             #end if
         ]]>
     </command>
@@ -99,7 +103,7 @@
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
         </data>
         <collection name="transcripts" type="list">
-            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" />
+            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>
     </outputs>
     <tests>