# HG changeset patch
# User greg
# Date 1508173881 14400
# Node ID 0e1041ee1926229ab089ecedc90228793f23feba
# Parent  c2b9081064f0879d3d84dccc7a9e8d253f30c144
Uploaded

diff -r c2b9081064f0 -r 0e1041ee1926 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Fri Oct 13 14:24:30 2017 -0400
+++ b/gene_family_aligner.xml	Mon Oct 16 13:11:21 2017 -0400
@@ -106,11 +106,11 @@
         </collection>
         <collection name="trimmed_faa" type="list" label="${tool.name} (trimmed orthogroup protein alignments) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" />
-            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+            <filter>codon_alignments == 'no' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
         </collection>
         <collection name="filtered_faa" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
-            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+            <filter>codon_alignments == 'no' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
         <collection name="pristine_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />