# HG changeset patch
# User greg
# Date 1490273496 14400
# Node ID 79573009efe0380e4e66c444e434ec2fea537ba1
# Parent  6c1cfd0be856ab92baaad91300823d4bbe384830
Uploaded

diff -r 6c1cfd0be856 -r 79573009efe0 macros.xml
--- a/macros.xml	Thu Mar 23 08:30:55 2017 -0400
+++ b/macros.xml	Thu Mar 23 08:51:36 2017 -0400
@@ -74,6 +74,20 @@
             <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
         </param>
     </xml>
+    <xml name="cond_multiple_sequence_alignments_option_with_iterative_realignments">
+        <conditional name="multiple_sequence_alignments_option_cond">
+            <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
+                <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
+                <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
+                <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
+                <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option>
+            </param>
+            <expand macro="whens_multiple_sequence_alignments_option_cond" />
+            <when value="iterative_realignments">
+                <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="whens_multiple_sequence_alignments_option_cond">
         <when value="create_alignments" />
         <when value="add_alignments" />
@@ -93,6 +107,18 @@
             </when>
         </conditional>
     </xml>
+    <xml name="cond_multiple_sequence_alignments_with_iterative_realignments">
+        <conditional name="multiple_sequence_alignments_cond">
+            <expand macro="param_multiple_sequence_alignments" />
+            <when value="no" />
+            <when value="yes">
+                <conditional name="multiple_sequence_alignments_option_cond">
+                    <expand macro="whens_multiple_sequence_alignments_option_cond" />
+                    <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignments" />
+                </conditional>
+            </when>
+        </conditional>
+    </xml>
     <xml name="cond_phylogenetic_trees_ptortho">
         <conditional name="phylogenetic_trees_cond">
             <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
@@ -188,14 +214,15 @@
                         <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
-                    <when value="no" />
+                    <when value="no">
+                        <expand macro="cond_multiple_sequence_alignments" />
+                    </when>
                     <when value="yes">
                         <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
                         <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
-                        <expand macro="cond_multiple_sequence_alignments" />
+                        <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" />
                     </when>
                 </conditional>
-                <expand macro="cond_multiple_sequence_alignments" />
             </when>
         </conditional>
     </xml>