| Previous changeset 10:8923d4ea858b (2014-08-12) Next changeset 12:ebb4cb1e8e35 (2014-10-01) |
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Commit message:
- Removed max on cpm filtering. Really shouldn't have been there in the first place. - Added explicit arguments to processHairpinReads in R. |
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modified:
hairpinTool.R hairpinTool.xml |
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| diff -r 8923d4ea858b -r c0a76e30d61b hairpinTool.R --- a/hairpinTool.R Tue Aug 12 14:42:27 2014 +1000 +++ b/hairpinTool.R Tue Sep 30 16:36:12 2014 +1000 |
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| @@ -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) |
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| diff -r 8923d4ea858b -r c0a76e30d61b hairpinTool.xml --- a/hairpinTool.xml Tue Aug 12 14:42:27 2014 +1000 +++ b/hairpinTool.xml Tue Sep 30 16:36:12 2014 +1000 |
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| @@ -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" |