# HG changeset patch
# User greg
# Date 1490295687 14400
# Node ID 56dbe45f4bfb8a0623ba5f3807fcd6dbc095063b
# Parent  7389c8a99491af050d2b70bfd69e45a8123d540a
Uploaded

diff -r 7389c8a99491 -r 56dbe45f4bfb macros.xml
--- a/macros.xml	Thu Mar 23 11:54:44 2017 -0400
+++ b/macros.xml	Thu Mar 23 15:01:27 2017 -0400
@@ -13,6 +13,71 @@
             <regex match="Exception:"/>
         </stdio>
     </xml>
+    <token name="@REMOVE_GAPPY_SEQUENCES_COND@">
+        #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) == 'no':
+            #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond
+            #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
+            #if str($multiple_sequence_alignments) == 'yes':
+                #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
+                #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
+                #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+                    #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
+                #end if
+            #end if
+        #else:
+            #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':
+                #set gap_trimming = $trim_type_cond.gap_trimming
+            #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) == 'no':
+                #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond
+                #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
+                #if str($multiple_sequence_alignments) == 'yes':
+                    #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
+                    #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
+                    #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+                        #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
+                    #end if
+                #end if
+            #else:
+                #set remove_sequences_with_gaps_of = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
+                #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond
+                #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
+                #if str($multiple_sequence_alignments) == 'yes':
+                    #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
+                    #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
+                    #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+                        #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
+                    #else if str($multiple_sequence_alignments_option) == 'iterative_realignments':
+                        #set iterative_realignments = $multiple_sequence_alignments_option_cond.iterative_realignments
+                    #end if
+                #end if
+            #end if
+        #end if
+    </token>
+    <token name="@SET_PHYLOGENETIC_TREES@">
+        #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
+        #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
+    </token>
+    <token name="@TREE_INFERENCE_COND@">
+        #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
+        #set tree_inference = $tree_inference_cond.tree_inference
+        #if str($tree_inference) == 'raxml':
+            #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
+            #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
+            #if str($rooting_order_file) == 'yes':
+                #set rooting_order = $rooting_order_file_cond.rooting_order
+            #end if
+            #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
+        #end if
+        #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size
+        #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size
+    </token>
     <xml name="param_scaffold">
         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
@@ -202,10 +267,10 @@
                         <option value="gap_trimming" selected="true">Nucleotide based </option>
                         <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
                     </param>
-                    <when value="automated_trimming" />
                     <when value="gap_trimming">
                         <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
                     </when>
+                    <when value="automated_trimming" />
                 </conditional>
                 <conditional name="remove_sequences_with_gaps_cond">
                     <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
diff -r 7389c8a99491 -r 56dbe45f4bfb phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Mar 23 11:54:44 2017 -0400
+++ b/phylogenomics_analysis.xml	Thu Mar 23 15:01:27 2017 -0400
@@ -10,25 +10,50 @@
             #set input_format = $input_format_cond.input_format
             #set scaffold = $input_format_cond.scaffold
             #set method = $input_format_cond.method
-            #set options_type_cond = $input_format_cond.options_type_cond
+
+            #if str($input_format) == 'ptortho':
+                #set options_type_cond = $input_format_cond.options_type_cond
+            #else:
+                #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
+                #set orthogroup_fna= $orthogroup_fna_cond.orthogroup_fna
+                #set options_type_cond = $orthogroup_fna_cond.options_type_cond
+            #endif
             #set options_type= $options_type_cond.options_type
 
             #if str($options_type) == 'advanced':
-                #set multiple_sequence_alignments_cond = $options_type_cond.multiple_sequence_alignments_cond
-                #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
-                #if str($multiple_sequence_alignments) == 'yes':
-                    #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
-                    #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
-                #end if
-                #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
-                #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
-                #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
-                #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
-                #if str(input_format) == 'ptortho':
-                    #set sequence_type = 'protein'
+                #if str($input_format) == 'ptortho':
+                    @REMOVE_GAPPY_SEQUENCES_COND@
+                    @SET_PHYLOGENETIC_TREES@
+                    #if str($phylogenetic_trees) == 'yes':
+                        @TREE_INFERENCE_COND@
+                        #set sequence_type = 'protein'
+                    #end if
                 #else:
-                    #set sequence_type = $phylogenetic_trees_cond.sequence_type
-                    #set orthogroup_fna = $input_format_cond.orthogroup_fna
+                    ## str($input_format) == 'ptorthocs'
+                    #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
+                    #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna
+                    #set options_type_cond = orthogroup_fna_cond.options_type_cond
+                    #set options_type = $options_type_cond.options_type
+                    #if str($orthogroup_fna) == 'yes':
+                        #if str(options_type) == 'advanced':
+                            @REMOVE_GAPPY_SEQUENCES_COND@
+                            #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
+                            @SET_PHYLOGENETIC_TREES@
+                            #if str($phylogenetic_trees) == 'yes':
+                                @TREE_INFERENCE_COND@
+                                #set sequence_type = $phylogenetic_trees_cond.sequence_type
+                            #end if
+                        #end if
+                    #else:
+                        #if str(options_type) == 'advanced':
+                            @REMOVE_GAPPY_SEQUENCES_COND@
+                            @SET_PHYLOGENETIC_TREES@
+                            #if str($phylogenetic_trees) == 'yes':
+                                @TREE_INFERENCE_COND@
+                                #set sequence_type = $phylogenetic_trees_cond.sequence_type
+                            #end if
+                        #end if
+                    #end if
                 #end if
             #end if
 
@@ -60,12 +85,8 @@
                 #end if
 
                 #if str($phylogenetic_trees) == 'yes':
-                    #set tree_inference_cond = $options_type_cond.phylogenetic_trees_cond.tree_inference_cond
-                    #set tree_inference_method = $tree_inference_cond.tree_inference
-                    --tree_inference $tree_inference_method
-                    #if str($tree_inference_method) == 'raxml':
-                        #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
-                        #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
+                    --tree_inference $tree_inference
+                    #if str($tree_inference) == 'raxml':
                         #if str($rooting_order_file) == 'yes':
                             --rooting_order '$rooting_order_file_cond.rooting_order'
                             # No else block needed here because the default rooting_order
@@ -79,10 +100,6 @@
                 #end if
 
                 #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
-                    #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
                     #end if
@@ -126,8 +143,8 @@
                     <expand macro="param_options_type" />
                     <when value="basic" />
                     <when value="advanced">
+                        <expand macro="cond_remove_gappy_sequences" />
                         <expand macro="cond_phylogenetic_trees_ptortho" />
-                        <expand macro="cond_remove_gappy_sequences" />
                     </when>
                 </conditional>
             </when>