# HG changeset patch
# User stef
# Date 1403082310 14400
# Node ID 9f4e0192de1005e0c49d96f90ba5565157424101
# Parent  5f8b99ae75efd6d1db1e1a6785b4ee86fa27b7b4
Uploaded

diff -r 5f8b99ae75ef -r 9f4e0192de10 QDNAseq.xml
--- a/QDNAseq.xml	Wed Jun 18 04:46:56 2014 -0400
+++ b/QDNAseq.xml	Wed Jun 18 05:05:10 2014 -0400
@@ -1,9 +1,10 @@
 <tool id="QDNAseq" name="QDNAseq" version="0.0.1">
   
   <requirements>
-    <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement>
-    <requirement type="package" version="3.0.3">R</requirement>
-    <requirement type="package" version="1.0.4">bioc_qdnaseq</requirement>
+    <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> -->
+    <!-- The R package for v3.1.0 is not ready yet -->
+    <!--<requirement type="package" version="3.1.0">R</requirement>-->
+    <!-- <requirement type="package" version="1.0.5">bioc_qdnaseq</requirement> -->
   </requirements>
 
   <description>Quantitative copy number abberation detection</description>
@@ -26,7 +27,6 @@
     <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
       <validator type="empty_field" />
       <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
-      <!-- <validator type="expression" message="Window Size must be even">value % 2 ==0</validator> -->
     </param>
     <param name="binSize" type="select" label="Select bin-size to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
       <option value="1000">1Mb</option>
@@ -44,13 +44,6 @@
       <option value="SR50">Single Read 50bp</option>
       <!-- <option value="PE1000">PairedEnd1000</option> -->
     </param>
-    
-    <!--
-    <param name="excludeChrs" type="select" multiple="true" label="Exclude certain Chromosomes">
-      <option value="X">X</option>
-      <option value="Y">Y</option>
-    </param>
-    -->
 
     <!-- ==================== -->
     <!-- Input BAMs -->
@@ -265,18 +258,11 @@
   <!-- 
   <tests>
     <test>
-      <param name="input1" value="5.bed" />
-      <param name="distance" value="1" />
-      <param name="minregions" value="2" />
-      <param name="returntype" value="1" />
-      <output name="output" file="gops-cluster-1.bed" />     
+      <param name="input1" value="input1" />   
+      <param name="input2" value="input2" />   
     </test>
   </tests>
   -->
-  <!-- <requirements>
-      <requirement type="package">ucsc_tools</requirement>
-  </requirements>
--->
 
   <help>
 .. class:: infomark
@@ -316,6 +302,9 @@
 For the underlying tool please cite: llari Scheinin, Daoud Sie et al. DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions, (submitted). See also the bioconductor package_ documentation.
 
 .. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+
+
+.. image:: no_image.png
   </help>
 
-</tool>
\ No newline at end of file
+</tool>