Mercurial > repos > greg > phylogenomics_analysis

changeset 90:6c1cfd0be856 draft

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Uploaded
author greg
date Thu, 23 Mar 2017 08:30:55 -0400
parents 0fc75cdc686a
children 79573009efe0
files macros.xml
diffstat 1 files changed, 23 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Mar 23 08:19:44 2017 -0400
+++ b/macros.xml	Thu Mar 23 08:30:55 2017 -0400
@@ -61,25 +61,34 @@
             </when>
         </conditional>
     </xml>
+    <xml name="param_multiple_sequence_alignments">
+        <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </xml>
+    <xml name="param_multiple_sequence_alignments_option">
+        <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>
+        </param>
+    </xml>
+    <xml name="whens_multiple_sequence_alignments_option_cond">
+        <when value="create_alignments" />
+        <when value="add_alignments" />
+        <when value="pasta_alignments">
+            <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
+        </when>
+    </xml>
     <xml name="cond_multiple_sequence_alignments">
         <conditional name="multiple_sequence_alignments_cond">
-            <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
+            <expand macro="param_multiple_sequence_alignments" />
             <when value="no" />
             <when value="yes">
                 <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>
-                    </param>
-                    <when value="create_alignments" />
-                    <when value="add_alignments" />
-                    <when value="pasta_alignments">
-                        <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
-                    </when>
+                    <expand macro="whens_multiple_sequence_alignments_option_cond" />
+                    <expand macro="param_multiple_sequence_alignments_option" />
                 </conditional>
             </when>
         </conditional>