# HG changeset patch
# User greg
# Date 1491845787 14400
# Node ID 5ad5d4204edf8f6c107e5e82f1cab7a81ba64073
# Parent  43341e97bb089bcf6f735e6fd17e532800eb8634
Uploaded

diff -r 43341e97bb08 -r 5ad5d4204edf gene_family_aligner.xml
--- a/gene_family_aligner.xml	Mon Apr 10 12:47:18 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 13:36:27 2017 -0400
@@ -44,19 +44,39 @@
                     #if str($remove_sequences_with_gaps) == 'yes':
                         --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
                         --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
-                        --output '$output_aln_filtered'
-                        --output_dir '$output_aln_filtered.files_path'
+                        #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
+                            --output '$output_aln_filtered'
+                            --output_dir '$output_aln_filtered.files_path'
+                        #else:
+                            --output '$output_aln_filtered_ca'
+                            --output_dir '$output_aln_filtered_ca.files_path'
+                        #end if
                     #else:
-                        --output '$output_aln_trimmed'
-                        --output_dir '$output_aln_trimmed.files_path'
+                        #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
+                            --output '$output_aln_trimmed'
+                            --output_dir '$output_aln_trimmed.files_path'
+                        #else:
+                            --output '$output_aln_trimmed_ca'
+                            --output_dir '$output_aln_trimmed_ca.files_path'
+                        #end if
                     #end if
                 #else:
+                    #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
+                        --output '$output_aln'
+                        --output_dir '$output_aln.files_path'
+                    #else:
+                        --output '$output_aln_ca'
+                        --output_dir '$output_aln_ca.files_path'
+                    #end if
+                #end if
+            #esle:
+                #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
                     --output '$output_aln'
                     --output_dir '$output_aln.files_path'
+                #else:
+                    --output '$output_aln_ca'
+                    --output_dir '$output_aln_ca.files_path'
                 #end if
-            #esle:
-                --output '$output_aln'
-                --output_dir '$output_aln.files_path'
             #end if
         ]]>
     </command>
@@ -86,13 +106,22 @@
     </inputs>
     <outputs>
         <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
-            <filter>options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no')</filter>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter>
+        </data>
+        <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}">
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter>
         </data>
         <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
-            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+        </data>
+        <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}">
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </data>
         <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
-            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
+        </data>
+        <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}">
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
         </data>
     </outputs>
     <tests>