# HG changeset patch
# User stef
# Date 1403195746 14400
# Node ID 327b8830d49f1f847e0082c9c753a72cad665cb8
# Parent  4351c77152751ca2e49e9b3b6ed7ca9982aa39be
Uploaded

diff -r 4351c7715275 -r 327b8830d49f QDNAseq.xml
--- a/QDNAseq.xml	Thu Jun 19 12:35:36 2014 -0400
+++ b/QDNAseq.xml	Thu Jun 19 12:35:46 2014 -0400
@@ -47,25 +47,22 @@
       <option value="5">5kb</option>
       <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 Read 50bp</option>
+      <option value="SR50">Single Reads of 50bp</option>
       <!-- <option value="PE1000">PairedEnd1000</option> -->
     </param>
 
     <!-- ==================== -->
     <!-- Input BAMs -->
     <!-- ==================== -->
-    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select all BAM files to include in the analysis" />
+    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
 
     <!-- ==================== -->
     <!-- This section contains galaxy history output settings -->
     <!-- ==================== -->
     <conditional name="extra_history_outputs">
-      <param name="show" type="select" label="Show additional history outputs">
+      <param name="show" type="select" label="Optional history outputs">
         <option value="NO">Only output Report to history</option>
         <option value="YES">Select additional history outputs</option>
       </param>
@@ -114,6 +111,10 @@
         <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>
@@ -137,6 +138,7 @@
       </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" />
@@ -204,12 +206,12 @@
 "${jobName}" -> outputName
 
 ## extra params
-as.logical( "${doCall}" ) -> doCall
 "${htmlFile}" -> outputHtml
 "${htmlFile.files_path}" -> outputPath
 "${use_own_binannotation.binannotation_file}" -> binAnnotations
 
 ## advanced options
+as.logical( "${advanced.doCall}" ) -> doCall
 as.double( "${advanced.undoSD}" ) -> undoSD
 as.logical( "${advanced.debug}" ) -> debug
 as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
@@ -286,11 +288,15 @@
 
 It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.
 
+For questions/remarks about the galaxy part of this tool, see contact form here_
+
+.. _here: http://www.stefs.nl/wp/contact
+
 -----
 
 .. class:: warningmark
 
-As there is no R 3.1.0 package yet which is required, the **dependencies** need to be installed by hand and available to the galaxy user: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5)
+As there is no R 3.1.0 package yet (which is required), the **dependencies** need to be installed by hand and available to the user under which galaxy runs: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5)
 
 .. class:: warningmark
 
@@ -310,6 +316,7 @@
 
 
 .. image:: LGG150_copynumber_example.png
+.. image:: LGG150_calls_example.png
   </help>
 
 </tool>