# HG changeset patch
# User dcorreia
# Date 1477568694 14400
# Node ID 52238a3c477392ffa66b8fd6193ce2efbe173888
# Parent  3b7dde5c3ec40b314a697161380015c2bf70a07f
Uploaded

diff -r 3b7dde5c3ec4 -r 52238a3c4773 noisy.xml
--- a/noisy.xml	Wed Mar 23 06:49:51 2016 -0400
+++ b/noisy.xml	Thu Oct 27 07:44:54 2016 -0400
@@ -5,21 +5,8 @@
     </requirements>
     <command><![CDATA[ 
                 noisy $input
-                
-                 #if $sequence.seqtype == 'cfg' :
-	                 ## Automatic sequence detection
-	                 ## read an info file to choose which option set 
-	                 #set $info = open( str($input_info) ).read()
-	                 #if 'dna' in $info:
-	                        --seqtype D
-	                 #else if 'protein' in $info :
-	                        --seqtype P
-	                 #end if
-	                 
-                 #else :
-                    --seqtype $sequence.seqtype
-                 #end if 
-                 
+
+                 --seqtype $seqtype
                  --cutoff $cutoff
                  --distance $distance
                  #if $usematrix.matrix == "true":
@@ -48,20 +35,11 @@
     </command>
 	<inputs>
 		<param name="input" type="data" format="fasta" label="Source file" help="Fasta format" />
-		<conditional name="sequence">
-			<param name="seqtype" type="select" label="Sequence Coding">
-				<option value="D">DNA</option>
-				<option value="P">Protein</option>
-				<option value="R">RNA</option>
-				<option value="cfg">Config file</option>
-			</param>
-			<when value="D"></when>
-			<when value="P"></when>
-			<when value="R"></when>
-			<when value="cfg">
-                <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" />
-            </when>	
-		</conditional>   
+        <param name="seqtype" type="select" label="Sequence Coding">
+            <option value="D">DNA</option>
+            <option value="P">Protein</option>
+            <option value="R">RNA</option>
+        </param>
 		<param name="cutoff" type="float" value="0.8" min="0" max="1" label="cut-off  [ 0-1 ]" help="Columns with a score below FLOAT are removed from the output alignment." />
 		<param name="distance" type="select" label="Distance methode used by NeighbotNet">
 		    <option value="HAMMING">HAMMING</option>
@@ -91,7 +69,7 @@
 	         </param>
             <when value="nnet"/>
             <when value="qnet"/>
-            <option value="all"/>
+            <when value="all"/>
             <when value="rand">
                 <param name="randpermut" type="integer" value="1000" label="random permutation"/>
             </when>