diff chipseeker.xml @ 7:1b9a9409831d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit e07ee851144e07fde91877727d6a39a1906f7639

--- 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