Mercurial > repos > stef > qdnaseq

changeset 6:beb7abe277b3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author stef
date Fri, 13 Jun 2014 11:01:25 -0400
parents d4747215fa6b
children 2671b48cc122
files QDNAseq.xml
diffstat 1 files changed, 4 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/QDNAseq.xml	Fri Jun 13 09:53:08 2014 -0400
+++ b/QDNAseq.xml	Fri Jun 13 11:01:25 2014 -0400
@@ -1,8 +1,9 @@
 <tool id="QDNAseq" name="QDNAseq" version="0.0.1">
   
   <requirements>
-    <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> -->
+    <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement>
     <requirement type="package" version="3.0.3">R</requirement>
+    <requirement type="package" version="1.0.4">bioc_qdnaseq</requirement>
   </requirements>
 
   <description>Quantitative copy number abberation detection</description>
@@ -292,24 +293,16 @@
 
 .. class:: warningmark
 
-Requires internet access for downloading bin-annotations from bitbucket and to show css styling of the final report
+The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.
 
 .. class:: warningmark
 
-All R stderr is rerouted to stdout due to limitations in R. This means the tool might be marked succesful (green) while it actually isn't, closer inspection of the stdout output is required in that case.
-
-.. class:: warningmark
-
-The smaller the binsize, the longer the analysis takes
+Requires **internet access** for downloading bin-annotations from bitbucket and to show css styling of the final report
 
 .. class:: warningmark
 
 If the data is noisy, a **larger binsize** should be chosen
 
-.. class:: warningmark
-
-The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.
-
 -----
 
 **Example**