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changeset 15:194e3f2c1d86 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
author iuc
date Tue, 09 Jul 2019 18:46:09 -0400
parents c97a786e8fb5
children 163688bb8f73
files diffbind.R diffbind.xml
diffstat 2 files changed, 8 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/diffbind.R	Thu Jun 07 05:21:22 2018 -0400
+++ b/diffbind.R	Tue Jul 09 18:46:09 2019 -0400
@@ -57,16 +57,15 @@
                         bamReads=bams,
                         bamControl=ctrls,
                         Peaks=peaks,
-                        Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot
-                        stringsAsFactors=FALSE)
+                        Tissue=samples) # using "Tissue" column to display ids as labels in PCA plot
 } else {
+
     sampleTable <- data.frame(SampleID=samples,
                         Replicate=samples,
                         Condition=groups,
                         bamReads=bams,
                         Peaks=peaks,
-                        Tissue=samples,
-                        stringsAsFactors=FALSE)
+                        Tissue=samples)
 }
 
 sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter)
@@ -126,7 +125,7 @@
         Strand=gsub("\\*", ".", strand(resSorted)),
         mcols(resSorted))
 }
-write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE)
+write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, row.names = FALSE)
 
 # Output binding affinity scores
 if (!is.null(opt$bmatrix)) {
--- a/diffbind.xml	Thu Jun 07 05:21:22 2018 -0400
+++ b/diffbind.xml	Tue Jul 09 18:46:09 2019 -0400
@@ -1,9 +1,9 @@
-<tool id="diffbind" name="DiffBind" version="2.6.6.4">
+<tool id="diffbind" name="DiffBind" version="2.10.0">
     <description> differential binding analysis of ChIP-Seq peak data</description>
     <requirements>
-        <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="0.2.15">r-rjson</requirement>
+        <requirement type="package" version="2.10.0">bioconductor-diffbind</requirement>
+        <requirement type="package" version="1.20.3">r-getopt</requirement>
+        <requirement type="package" version="0.2.20">r-rjson</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"