diff QDNAseq.xml @ 27:f89205f51e27 draft default tip

Uploaded

--- a/QDNAseq.xml	Mon Jul 06 05:38:44 2015 -0400
+++ b/QDNAseq.xml	Mon Jul 06 05:41:08 2015 -0400
@@ -19,6 +19,8 @@
     \$QDNASEQ_PATH
   </command>
 
+  <version_command interpreter="Rscript">QDNAseq-version.R</version_command>
+
   <stdio>
     <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
     <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
@@ -274,22 +276,22 @@
     <!-- WHY does there seem to be no way to use split() within this code in galaxy!!! -->
     <!-- now have to fall back to using unique names within binSizes instead of just integers -->
     <!-- Problem with integers is that both "1" and "5" are also present in eg "15,100" -->
-    <data format="tsv" name="txt_1000" label="QDNAseq: ${jobName} txt 1000kb">
+    <data format="tabular" name="txt_1000" label="QDNAseq: ${jobName} txt 1000kb">
       <filter>( "bin1000kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_100" label="QDNAseq: ${jobName} txt 100kb">
+    <data format="tabular" name="txt_100" label="QDNAseq: ${jobName} txt 100kb">
       <filter>("bin100kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_30" label="QDNAseq: ${jobName} txt 30kb">
+    <data format="tabular" name="txt_30" label="QDNAseq: ${jobName} txt 30kb">
       <filter>("bin30kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_15" label="QDNAseq: ${jobName} txt 15kb">
+    <data format="tabular" name="txt_15" label="QDNAseq: ${jobName} txt 15kb">
       <filter>("bin15kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_5" label="QDNAseq: ${jobName} txt 5kb">
+    <data format="tabular" name="txt_5" label="QDNAseq: ${jobName} txt 5kb">
       <filter>("bin5kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_1" label="QDNAseq: ${jobName} txt 1kb">
+    <data format="tabular" name="txt_1" label="QDNAseq: ${jobName} txt 1kb">
       <filter>("bin1kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
 
@@ -356,7 +358,7 @@
 
 .. class:: warningmark
 
-Requires **internet access** for downloading bin-annotations from bitbucket and to show some styling (css) of the final report
+Some optional history input/output files are of format "rds" (file format to store a R object). This is not registered in galaxy by default, so has to be added to the available datatypes.
 
 -----