# HG changeset patch
# User greg
# Date 1491585566 14400
# Node ID 01c08c35d05146cf44a64c37267a39d419d7c3ac
# Parent  4f1c3b8c9ab177197d6b4c9081184f963b3eb4d8
Uploaded

diff -r 4f1c3b8c9ab1 -r 01c08c35d051 gene_family_aligner.py
--- a/gene_family_aligner.py	Fri Apr 07 13:13:38 2017 -0400
+++ b/gene_family_aligner.py	Fri Apr 07 13:19:26 2017 -0400
@@ -36,8 +36,8 @@
     if args.pasta_iter_limit is not None:
         cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
 cmd += ' --num_threads %d' % args.num_threads
-if args.orthogroup_fna is not None:
-    cmd += ' --orthogroup_fna'
+if args.codon_alignments is not None:
+    cmd += ' --codon_alignments'
 if args.automated_trimming is not None:
     cmd += ' --automated_trimming'
 if args.gap_trimming is not None:
diff -r 4f1c3b8c9ab1 -r 01c08c35d051 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Fri Apr 07 13:13:38 2017 -0400
+++ b/gene_family_aligner.xml	Fri Apr 07 13:19:26 2017 -0400
@@ -89,10 +89,10 @@
     </inputs>
     <outputs>
         <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
+            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')</filter>
         </data>
         <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>