# HG changeset patch
# User greg
# Date 1491849808 14400
# Node ID 19529df59e9dba38c67b2fe4cfc01a853095c979
# Parent  a2b29eb5459dd317d7c584c68d163f561c195127
Uploaded

diff -r a2b29eb5459d -r 19529df59e9d gene_family_aligner.xml
--- a/gene_family_aligner.xml	Mon Apr 10 13:49:04 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 14:43:28 2017 -0400
@@ -10,6 +10,13 @@
             #set input_format = $input_format_cond.input_format
             #set alignment_method_cond = $input_format_cond.alignment_method_cond
             #set alignment_method = $alignment_method_cond.alignment_method
+            #if str($input_format_cond.input_format) == 'ptortho':
+                #set output_codon_alignments == False
+            #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
+                #set output_codon_alignments == False
+            #else:
+                #set output_codon_alignments == True
+            #end if
 
             python $__tool_directory__/gene_family_aligner.py
             --alignment_method $alignment_method
@@ -27,55 +34,44 @@
                     --codon_alignments 'true'
                 #end if
             #end if
-            #if str($options_type_cond.options_type) == 'advanced':
-                #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
-                #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
-                #if str($remove_gappy_sequences) == 'yes':
-                    #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
-                    #set trim_type = $trim_type_cond.trim_type
-                    #if str($trim_type) == 'gap_trimming':
-                        --gap_trimming $trim_type_cond.gap_trimming
+            #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
+            #if str($remove_gappy_sequences) == 'yes':
+                #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
+                #set trim_type = $trim_type_cond.trim_type
+                #if str($trim_type) == 'gap_trimming':
+                    --gap_trimming $trim_type_cond.gap_trimming
+                #else:
+                    ## str($trim_type) == 'automated_trimming'
+                    --automated_trimming 'true'
+                #end if
+                #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
+                #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
+                #if str($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
+                    #if $output_codon_alignments:
+                        --output '$output_aln_filtered_ca'
+                        --output_dir '$output_aln_filtered_ca.files_path'
                     #else:
-                        ## str($trim_type) == 'automated_trimming'
-                        --automated_trimming 'true'
-                    #end if
-                    #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
-                    #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
-                    #if str($remove_sequences_with_gaps) == 'yes':
-                        --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
-                        --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
-                        #if str($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:
-                        #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 '$output_aln_trimmed_ca.files_path'
-                        #end if
+                        --output '$output_aln_filtered'
+                        --output_dir '$output_aln_filtered.files_path'
                     #end if
                 #else:
-                    #if str($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'
+                    #if $output_codon_alignments:
+                        --output '$output_aln_trimmed_ca'
+                        --output_dir '$output_aln_trimmed_ca.files_path'
                     #else:
-                        --output '$output_aln_ca'
-                        --output_dir '$output_aln_ca.files_path'
+                        --output '$output_aln_trimmed'
+                        --output_dir '$output_aln_trimmed.files_path'
                     #end if
                 #end if
-            #esle:
-                #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
+            #else:
+                #if $output_codon_alignments:
+                    --output '$output_aln_ca'
+                    --output_dir '$output_aln_ca.files_path'
+                #else:
                     --output '$output_aln'
                     --output_dir '$output_aln.files_path'
-                #else:
-                    --output '$output_aln_ca'
-                    --output_dir '$output_aln_ca.files_path'
                 #end if
             #end if
         ]]>
@@ -96,32 +92,26 @@
                 <expand macro="param_codon_alignments" />
             </when>
         </conditional>
-        <conditional name="options_type_cond">
-            <expand macro="param_options_type" />
-            <when value="basic" />
-            <when value="advanced">
-                <expand macro="cond_remove_gappy_sequences" />
-            </when>
-        </conditional>
+        <expand macro="cond_remove_gappy_sequences" />
     </inputs>
     <outputs>
         <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
-            <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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and 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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and 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>(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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['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>
         </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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) 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>
         </data>
         <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
-            <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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['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>
         </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>
+            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) 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>
         </data>
     </outputs>
     <tests>