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diff diamand.xml @ 2:09a565cfc192 draft

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Uploaded
author bgruening
date Sat, 07 Feb 2015 12:19:45 -0500
parents fbe4eedec466
children e1326442d13f
line wrap: on
line diff
--- a/diamand.xml	Sat Feb 07 05:32:30 2015 -0500
+++ b/diamand.xml	Sat Feb 07 12:19:45 2015 -0500
@@ -47,20 +47,6 @@
 ]]>
     </command>
     <inputs>
-        <conditional name="method">
-            <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
-                <option value="blastp">Align amino acid query sequences (blastp)</option>
-                <option value="blastx">Align DNA query sequences (blastx)</option>
-            </param>
-            <when value="blastp">
-                <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
-                <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
-            </when>
-            <when value="blastx">
-                <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
-                <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
-            </when>
-        </conditional>
 
         <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />
 
@@ -85,6 +71,21 @@
           </when>  <!-- history -->
         </conditional>
 
+        <conditional name="method">
+            <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
+                <option value="blastp">Align amino acid query sequences (blastp)</option>
+                <option value="blastx">Align DNA query sequences (blastx)</option>
+            </param>
+            <when value="blastp">
+                <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
+                <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
+            </when>
+            <when value="blastx">
+                <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
+                <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
+            </when>
+        </conditional>
+
         <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)">
             <option value="BLOSUM45">BLOSUM45</option>
             <option value="BLOSUM50">BLOSUM50</option>