# HG changeset patch
# User rnateam
# Date 1543231297 18000
# Node ID 90fe78a19b554167419c284e82daaffd8362322e
# Parent  535321abf9a463f7116979c494eb1df685b7bb69
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 6f594126ac7369cc80c30a02a6df57e785dfb45a

diff -r 535321abf9a4 -r 90fe78a19b55 chipseeker.R
--- a/chipseeker.R	Fri Jun 01 02:13:33 2018 -0400
+++ b/chipseeker.R	Mon Nov 26 06:21:37 2018 -0500
@@ -53,17 +53,18 @@
 # Convert from 1-based to 0-based format
 if (format == "interval") {
     metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|"))
-    resout <- data.frame(Chrom=res$seqnames,
-                    Start=res$start - 1,
-                    End=res$end,
-                    Comment=metacols)
+    resout <- data.frame(res$seqnames,
+                    res$start - 1,
+                    res$end,
+                    metacols)
+    colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
 } else {
-    resout <- data.frame(Chrom=res$seqnames,
-                    Start=res$start - 1,
-                    End=res$end,
+    resout <- data.frame(res$seqnames,
+                    res$start - 1,
+                    res$end,
                     metacols)
+    colnames(resout)[1:3] <- c("Chrom", "Start", "End")
 }
-
 write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE)
 
 if (!is.null(args$plots)) {
diff -r 535321abf9a4 -r 90fe78a19b55 chipseeker.xml
--- a/chipseeker.xml	Fri Jun 01 02:13:33 2018 -0400
+++ b/chipseeker.xml	Mon Nov 26 06:21:37 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="chipseeker" name="ChIPseeker" version="1.14.2.2">
+<tool id="chipseeker" name="ChIPseeker" version="1.16.1">
     <description>for ChIP peak annotation and visualization</description>
     <requirements>
-        <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement>
+        <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement>
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <version_command><![CDATA[