--- a/chipseeker.R	Wed Mar 13 03:05:16 2019 -0400
+++ b/chipseeker.R	Sat Apr 27 11:04:35 2019 -0400
@@ -12,6 +12,7 @@
 
 option_list <- list(
     make_option(c("-i","--infile"), type="character", help="Peaks file to be annotated"),
+    make_option(c("-H","--header"), type="logical", help="Peaks file contains header row"),
     make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
     make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
     make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
@@ -51,7 +52,13 @@
     ignoreDownstream <- FALSE
 }
 
-peaks <- readPeakFile(peaks)
+if (!is.null(args$header)) {
+    header <- TRUE
+} else {
+    header <- FALSE
+}
+
+peaks <- readPeakFile(peaks, header=header)
 
 # Make TxDb from GTF
 txdb <- makeTxDbFromGFF(gtf, format="gtf")
@@ -93,11 +100,14 @@
 if (!is.null(args$plots)) {
     pdf("out.pdf", width=14)
     plotAnnoPie(peakAnno)
-    plotAnnoBar(peakAnno)
+    p1 <- plotAnnoBar(peakAnno)
+    print(p1)
     vennpie(peakAnno)
     upsetplot(peakAnno)
-    plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
+    p2 <- plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
+    print(p2)
     dev.off()
+    rm(p1, p2)
 }
 
 ## Output RData file

--- a/chipseeker.xml	Wed Mar 13 03:05:16 2019 -0400
+++ b/chipseeker.xml	Sat Apr 27 11:04:35 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="chipseeker" name="ChIPseeker" version="1.18.0">
+<tool id="chipseeker" name="ChIPseeker" version="1.18.0+galaxy1">
     <description>for ChIP peak annotation and visualization</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-chipseeker</requirement>
@@ -22,6 +22,7 @@
         Rscript '$__tool_directory__/chipseeker.R'
 
         -i '$peaks'
+        -H $header
         -G '$gtf'
         -u $adv.upstream
         -d $adv.downstream
@@ -51,6 +52,7 @@
     </command>
     <inputs>
         <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
+        <param name="header" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Peaks file has header?" help="If this option is set to Yes, the tool will assume that the peak file has column headers in the first row. Default: No" />
         <conditional name="gtf_source">
             <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
                 <option value="cached" selected="true">Use a built-in GTF</option>
@@ -189,7 +191,7 @@
 
 **Inputs**
 
-A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
+A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. Note that there is an option to specify if the input peaks file has a header row. No header row is assumed by default, which is usually the case for BED format e.g. MACS narrowpeak, however other formats e.g. MACS tabular format, may contain a header row.
 
 Example:
 
@@ -212,7 +214,7 @@
 This tool outputs
 
     * a file of annotated peaks in Interval or Tabular format
-    * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
+    * a PDF of plots (plotAnnoPie, plotAnnoBar, vennpie, upsetplot, plotDistToTSS)
 
 Optionally, you can choose to output