diff phylogenomics_analysis.xml @ 28:a401feff8354 draft

Uploaded

--- a/phylogenomics_analysis.xml	Tue Jan 10 12:21:47 2017 -0500
+++ b/phylogenomics_analysis.xml	Tue Jan 10 12:26:30 2017 -0500
@@ -71,6 +71,7 @@
                     #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
                         #set multiple_sequence_alignments_option_str = 'Create alignments (PASTA algorithm)'
                     #end if
+
                     #set input_includes_coding_sequences_cond = $options_type.multiple_sequence_alignments_cond.input_includes_coding_sequences_cond
                     #set input_includes_coding_sequences = $input_includes_coding_sequences_cond.input_includes_coding_sequences
                     #if str($input_includes_coding_sequences) == 'yes':
@@ -79,6 +80,7 @@
                         #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
                         #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
                     #end if
+
                     #if str($multiple_sequence_alignments_option) == 'create_alignments':
                         --create_alignments
                     #else if str($multiple_sequence_alignments_option) == 'add_alignments':
@@ -87,6 +89,7 @@
                         --pasta_alignments
                         --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
                     #end if
+
                     #if str($input_includes_coding_sequences) == 'yes':
                         #if str($multiple_codon_alignments) == 'yes':
                             --codon_alignments
@@ -283,7 +286,7 @@
     </inputs>
     <outputs>
         <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
-        <data name="output_aln" format="txt" label="Multiple sequence alignments using method '${multiple_sequence_alignments_option_str}' on ${on_string}">
+        <data name="output_aln" format="txt" label="${multiple_sequence_alignments_option_str} on ${on_string}">
             <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}">