changeset 60:792435073fe1 draft

Uploaded

--- a/QDNAseq.xml	Thu Aug 07 11:02:25 2014 -0400
+++ b/QDNAseq.xml	Thu Aug 07 11:02:44 2014 -0400
@@ -11,7 +11,7 @@
 
   <!-- command block to call script with default R environment -->
   <!-- change interpreter to /full/path/to/Rscript if required -->
-  <command interpreter="Rscript"> 
+  <command interpreter="/ccagc/lib/R/R-3.1.0/bin/Rscript"> 
     QDNAseq.R 
     $qdnaseq_cfg
   </command>
@@ -39,7 +39,7 @@
       <option value="1">1kb</option>
     </param>
 
-    <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
+    <param name="doCall" type="select" label="Also segment and call with CGHcall" help="Segmenting and calling can take significant computational time">
       <option value="TRUE">yes</option>
       <option value="FALSE">no</option>
     </param>
@@ -76,10 +76,15 @@
           <option value="TRUE">yes</option>
         </param>
       </when>
+      <param name="copynumbers_igv" type="select" label="Also output copynumbers IGV file to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
       <when value="NO">
         <param name="readcounts_rds" type="hidden" value="FALSE" />
         <param name="copynumbers_rds" type="hidden" value="FALSE" />
         <param name="calls_rds" type="hidden" value="FALSE" />
+        <param name="copynumbers_igv" type="hidden" value="FALSE" />
       </when>
     </conditional>
 
@@ -213,9 +218,11 @@
 as.logical( "${extra_history_outputs.readcounts_rds}" ) -> doOutputReadcountsRds
 as.logical( "${extra_history_outputs.copynumbers_rds}" ) -> doOutputCopynumbersRds
 as.logical( "${extra_history_outputs.calls_rds}" ) -> doOutputCallsRds
+as.logical( "${extra_history_outputs.copynumbers_igv}" ) -> doOutputCopynumbersIgv
 "${rdsReadCounts}" -> readCountsDatasetFile
 "${rdsCopyNumbers}" -> copyNumbersDatasetFile
 "${rdsCalls}" -> calledSegmentsDatasetFile
+"${igvCopyNumbers}" -> copyNumbersIgvDatasetFile
 
 ## plotting params
 as.integer( "${plot_options.plot_width}" ) -> PLOT_WIDTH
@@ -253,6 +260,10 @@
       <filter> extra_history_outputs['calls_rds'] == "TRUE" </filter>
     </data>
 
+    <data format="txt" name="igvCopyNumbers" label="${jobName}_copyNumbers_${binSize}kb.igv">
+      <filter> extra_history_outputs['copynumbers_igv'] == "TRUE" </filter>
+    </data>
+
   </outputs>
 
   <!-- ==================== -->