# HG changeset patch
# User stef
# Date 1409929561 14400
# Node ID 41387ffa145f160d12c4be1ed484d1f8b23b2f79
# Parent  1f17446203d813cde0867eed1a37761cba8dd321
Uploaded

diff -r 1f17446203d8 -r 41387ffa145f QDNAseq.xml
--- a/QDNAseq.xml	Fri Sep 05 10:41:06 2014 -0400
+++ b/QDNAseq.xml	Fri Sep 05 11:06:01 2014 -0400
@@ -3,14 +3,13 @@
   <requirements>
     
     <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command -->
-    <requirement type="package" version="3.1.0">R</requirement>
+    <!-- <requirement type="package" version="3.1.0">R</requirement> -->
     <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> -->
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
 
   <description>Quantitative copy number abberation detection</description>
 
-  <!-- command block to call script with default R installation -->
   <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
   <command interpreter="Rscript"> 
     QDNAseq.R 
@@ -38,9 +37,9 @@
     <!-- Bin Size: only certain sizes are supported by QDNAseq package -->
     <param name="binSizes" type="select" optional="false" multiple="true" label="Select bin-sizes to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
       <option value="1000" selected="true">1Mb</option>
-      <option value="100">100kb</option>
+      <option value="100" selected="true">100kb</option>
       <option value="30">30kb</option>
-      <option value="15">15kb</option>
+      <option value="15" selected="true">15kb</option>
       <option value="5">5kb</option>
       <option value="1">1kb</option>
     </param>
diff -r 1f17446203d8 -r 41387ffa145f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 05 10:41:06 2014 -0400
+++ b/tool_dependencies.xml	Fri Sep 05 11:06:01 2014 -0400
@@ -5,20 +5,21 @@
         <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
     </package>
 
-    <!-- As soon as R 3_1_0 package works, all QDNAseq dependencies will be set via "package_qdnaseq_1_0_5" -->
-    <!-- Now this depency has to be manually installed by installing Bioconductor package "QDNAseq" -->
+    <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" -->
+    <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" -->
     
+    <!--
     <package name="R" version="3.1.0">
         <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
     </package>
-    
+    -->
+
     <!--
     <package name="qdnaseq" version="1.0.5">
         <repository name="package_qdnaseq_1_0_5" owner="stef"/>
     </package>
     -->
 
-    <!-- environment variable not in use now -->
     <!--
     <action type="set_environment">
         <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>