# HG changeset patch
# User greg
# Date 1504705963 14400
# Node ID cebcf6f7cff2f42611f8ae1ee87ff97e3904cffa
# Parent  d02010937c05a397af8a54bdc6d1e8111754c6e4
Uploaded

diff -r d02010937c05 -r cebcf6f7cff2 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Wed Sep 06 09:32:12 2017 -0400
+++ b/gene_family_aligner.xml	Wed Sep 06 09:52:43 2017 -0400
@@ -70,23 +70,23 @@
     </inputs>
     <outputs>
         <collection name="primary" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
         </collection>
         <collection name="trimmed" type="list" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
         </collection>
         <collection name="primary_trimmed" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
         </collection>
         <collection name="filtered" type="list" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
         <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
     </outputs>