diff QDNAseq.xml @ 67:2d939f4c23fe draft

Uploaded

--- a/QDNAseq.xml	Wed Aug 20 11:22:43 2014 -0400
+++ b/QDNAseq.xml	Tue Aug 26 07:38:40 2014 -0400
@@ -6,14 +6,13 @@
     <!-- <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>
-    <requirement type="set_environment">TOOL_DIR</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"> 
+  <command interpreter="/ccagc/lib/R/R-3.1.0/bin/Rscript"> 
     QDNAseq.R 
     $qdnaseq_cfg
   </command>
@@ -55,7 +54,7 @@
     <!-- ==================== -->
     <!-- Input BAMs -->
     <!-- ==================== -->
-    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
+    <param name="bams" type="data" multiple="true" optional="True" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
 
     <!-- ==================== -->
     <!-- Optional segmenting -->
@@ -284,7 +283,7 @@
 
 .. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
 
-.. image:: ./LGG150_copynumber_example.png :height: 240 :width: 480
+.. image:: LGG150_copynumber_example.png :height: 240 :width: 480
 
   </help>