# HG changeset patch
# User stef
# Date 1403094988 14400
# Node ID d5ed2f8fab83a65892d3581ae77cebc1c2812299
# Parent  40ae4457462480ae0b189d25b2d78bc7c4e2d319
Uploaded

diff -r 40ae44574624 -r d5ed2f8fab83 QDNAseq.xml
--- a/QDNAseq.xml	Wed Jun 18 07:45:19 2014 -0400
+++ b/QDNAseq.xml	Wed Jun 18 08:36:28 2014 -0400
@@ -3,23 +3,26 @@
   <requirements>
     <!-- <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="3.1.0">R</requirement>-->
+    <requirement type="package" version="0.1.18">samtools</requirement>
     <!-- <requirement type="package" version="1.0.5">bioc_qdnaseq</requirement> -->
   </requirements>
 
   <description>Quantitative copy number abberation detection</description>
   
-  <!-- 
-  if case you want to use a specific R installation use the commented command block and set correct path
+  <!-- command block to call script with specific R installation (set full paths) -->
+  <!--
   <command>
-     /ccagc/lib/R/R-3.1.0/bin/Rscript QDNAseq.R 
+    /full/path/to/Rscript 
+    /full/path/to/QDNAseq.R 
     $qdnaseq_cfg
   </command>
   -->
 
+  <!-- command block to call script with default R environment -->
   <command interpreter="Rscript">
     QDNAseq.R 
-    $qdnaseq_cfg <!-- use a tmp config file to pass all params to R by source() -->
+    $qdnaseq_cfg
   </command>
 
   <stdio>
@@ -127,7 +130,7 @@
 
         <param name="mappability" type="integer" value="0" min="0" max="100" label="Filter bins with lower mappability" help="Will exclude all bins will lower mappability than this number (0-100)" />
 
-        <param name="debug" type="select" label="DEBUG/TEST" help="Use inbuilt LGG data instead of input BAMs">
+        <param name="debug" type="select" label="DEBUG / TEST" help="Use inbuilt LGG data instead of input BAMs">
           <option value="FALSE">no</option>
           <option value="TRUE">yes</option>
         </param>