Mercurial > repos > iuc > deseq2

diff deseq2.R @ 11:25204a860b79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:04:12 -0500
parents 6f91b8ce6e07
children bd06df00180a
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--- a/deseq2.R	Tue Aug 01 17:20:46 2017 -0400
+++ b/deseq2.R	Sun Jan 28 04:04:12 2018 -0500
@@ -55,6 +55,7 @@
   "plots" , "p", 1, "character",
   "sample_table", "s", 1, "character",
   "tximport", "i", 0, "logical",
+  "txtype", "y", 1, "character",
   "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
   "fit_type", "t", 1, "integer",
   "many_contrasts", "m", 0, "logical",
@@ -238,7 +239,7 @@
     library("tximport")
     txiFiles <- as.character(sampleTable[,2])
     names(txiFiles) <- as.character(sampleTable[,1])
-    txi <- tximport(txiFiles, type="sailfish", tx2gene=tx2gene)
+    txi <- tximport(txiFiles, type=opt$txtype, tx2gene=tx2gene)
     dds <- DESeqDataSetFromTximport(txi,
                                     sampleTable[,3:ncol(sampleTable),drop=FALSE],
                                     designFormula)