# HG changeset patch
# User stef
# Date 1403262847 14400
# Node ID 4372afee310bff4e2dcb464cf47808a795cf3965
# Parent  327b8830d49f1f847e0082c9c753a72cad665cb8
Uploaded

diff -r 327b8830d49f -r 4372afee310b QDNAseq.xml
--- a/QDNAseq.xml	Thu Jun 19 12:35:46 2014 -0400
+++ b/QDNAseq.xml	Fri Jun 20 07:14:07 2014 -0400
@@ -48,6 +48,11 @@
       <option value="1">1kb</option>
     </param>
 
+    <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
+      <option value="TRUE">yes</option>
+      <option value="FALSE">no</option>
+    </param>
+
     <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
       <option value="SR50">Single Reads of 50bp</option>
       <!-- <option value="PE1000">PairedEnd1000</option> -->
@@ -111,10 +116,6 @@
         <option value="yes">yes</option>
       </param>
       <when value="yes">
-        <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
-          <option value="TRUE">yes</option>
-          <option value="FALSE">no</option>
-        </param>
         
         <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
           <option value="sdundo">sdundo</option>
@@ -138,7 +139,6 @@
       </when>
       <!-- need to set defaults because params are passed to R anyway -->
       <when value="no">
-        <param name="doCall" type="hidden" value="TRUE" />
         <param name="undoSD" type="hidden" value="1" />
         <param name="undo_splits" type="hidden" value="sdundo" />
         <param name="blacklist" type="hidden" value="TRUE" />
@@ -209,9 +209,9 @@
 "${htmlFile}" -> outputHtml
 "${htmlFile.files_path}" -> outputPath
 "${use_own_binannotation.binannotation_file}" -> binAnnotations
+as.logical( "${doCall}" ) -> doCall
 
 ## advanced options
-as.logical( "${advanced.doCall}" ) -> doCall
 as.double( "${advanced.undoSD}" ) -> undoSD
 as.logical( "${advanced.debug}" ) -> debug
 as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins