# HG changeset patch
# User greg
# Date 1483801097 18000
# Node ID bacaa8a6e45dc4679500340a5199a647db49966a
# Parent  86a469a50fc4227c11eace0e474707963a747645
Uploaded

diff -r 86a469a50fc4 -r bacaa8a6e45d phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Sat Jan 07 09:51:01 2017 -0500
+++ b/phylogenomics_analysis.xml	Sat Jan 07 09:58:17 2017 -0500
@@ -33,7 +33,7 @@
             #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
             #set dest_fasta_dir = $output_fasta.extra_files_path
 
-            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments':
+            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
                 #set generate_output_aln = True
                 #set src_aln_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_aln')
                 #set dest_aln_dir = $output_aln.extra_files_path
@@ -277,7 +277,7 @@
     <outputs>
         <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
         <data name="output_aln" format="txt" label="Sequence alignments and corresponding phylogenies using PASTA on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option'] == 'pasta_alignments'</filter>
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
         </data>
         <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>