# HG changeset patch
# User greg
# Date 1490196549 14400
# Node ID 063a39e397059a8bb84561ddf909607719a82d4f
# Parent  7170b072b40a603d62c1fac46eb85000810deb6d
Uploaded

diff -r 7170b072b40a -r 063a39e39705 macros.xml
--- a/macros.xml	Wed Mar 22 11:20:53 2017 -0400
+++ b/macros.xml	Wed Mar 22 11:29:09 2017 -0400
@@ -55,7 +55,7 @@
             </when>
         </conditional>
     </xml>
-    <xml name="cond_phylogenomic_trees_start">
+    <xml name="cond_phylogenomic_trees_ptortho">
         <conditional name="phylogenetic_trees_cond">
             <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
                 <option value="no" selected="true">No</option>
@@ -85,14 +85,43 @@
                 </conditional>
                 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
                 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
+            </when>
+        </conditional>
     </xml>
-    <xml name="param_sequence_type">
-        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
-            <option value="protein" selected="true">Amino acid based</option>
-            <option value="dna">Nucleotide based</option>
-        </param>
-    </xml>
-    <xml name="cond_phylogenomic_trees_end">
+    <xml name="cond_phylogenomic_trees_ptorthocs">
+        <conditional name="phylogenetic_trees_cond">
+            <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <conditional name="tree_inference_cond">
+                    <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
+                        <option value="raxml" selected="true">RAxML</option>
+                        <option value="fasttree">FastTree</option>
+                    </param>
+                    <when value="raxml">
+                        <conditional name="rooting_order_file_cond">
+                            <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
+                                <option value="no" selected="true">No</option>
+                                <option value="yes">Yes</option>
+                            </param>
+                            <when value="no" />
+                            <when value="yes">
+                                <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
+                            </when>
+                        </conditional>
+                        <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
+                    </when>
+                    <when value="fasttree" />
+                </conditional>
+                <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
+                <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
+                <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
+                    <option value="protein" selected="true">Amino acid based</option>
+                    <option value="dna">Nucleotide based</option>
+                </param>
             </when>
         </conditional>
     </xml>