Mercurial > repos > shians > shrnaseq

changeset 11:c0a76e30d61b

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- Removed max on cpm filtering. Really shouldn't have been there in the first place. - Added explicit arguments to processHairpinReads in R.
author shian_su <registertonysu@gmail.com>
date Tue, 30 Sep 2014 16:36:12 +1000
parents 8923d4ea858b
children ebb4cb1e8e35
files hairpinTool.R hairpinTool.xml
diffstat 2 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/hairpinTool.R	Tue Aug 12 14:42:27 2014 +1000
+++ b/hairpinTool.R	Tue Sep 30 16:36:12 2014 +1000
@@ -359,7 +359,9 @@
 if (inputType=="fastq") {
   # Use EdgeR hairpin process and capture outputs
   hpReadout <- capture.output(
-  data <- processHairpinReads(fastqPath, samplePath, annoPath,
+  data <- processHairpinReads(readfile=fastqPath, 
+                              barcodefile=samplePath, 
+                              hairpinfile=annoPath,
                               barcodeStart=barStart, barcodeEnd=barEnd,
                               hairpinStart=hpStart, hairpinEnd=hpEnd, 
                               verbose=TRUE)
--- a/hairpinTool.xml	Tue Aug 12 14:42:27 2014 +1000
+++ b/hairpinTool.xml	Tue Sep 30 16:36:12 2014 +1000
@@ -1,4 +1,4 @@
-<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.12">
+<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.13">
   <description>
     Analyse hairpin differential representation using edgeR
   </description>
@@ -135,7 +135,7 @@
       </param>
       
         <when value="yes">
-          <param name="cpmReq" type="float" value="0.5" min="0" max="1"
+          <param name="cpmReq" type="float" value="0.5" min="0"
                  label="Minimum CPM"/>
                  
           <param name="sampleReq" type="integer" value="1" min="0"