diff QDNAseq.xml @ 72:fb2dfd8ba417 draft

Uploaded

--- a/QDNAseq.xml	Wed Aug 27 04:56:37 2014 -0400
+++ b/QDNAseq.xml	Fri Sep 05 11:10:27 2014 -0400
@@ -10,7 +10,6 @@
 
   <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>
@@ -166,6 +165,7 @@
 ## -----
 ## required params
 ## -----
+TRUE -> inGalaxy 
 "${binSizes}" -> binSizesString
 "${experimentType}" -> experimentType
 "${jobName}" -> outputName