# HG changeset patch
# User kpbioteam
# Date 1529595488 14400
# Node ID 8d05c398fecd2923ce614c184f19680a4b410461
# Parent  0473a72c943ce5189ed573a49fec916bd656d7e8
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty

diff -r 0473a72c943c -r 8d05c398fecd chipeakanno_annopeaks.R
--- a/chipeakanno_annopeaks.R	Thu Jun 21 11:21:03 2018 -0400
+++ b/chipeakanno_annopeaks.R	Thu Jun 21 11:38:08 2018 -0400
@@ -11,12 +11,13 @@
 input2 = args[2]
 input3  = as.numeric(args[3])
 input4 = as.numeric(args[4])
+input5 = as.numeric(args[5])
 output1  = args[5]
 
 DMRInfo <-  read.table(input1)
 peaks <- GRanges(seqnames = DMRInfo[, 1],
                     ranges = IRanges
-                    (start = DMRInfo[, 2], end = DMRInfo[, 3]),score=DMRInfo[, 9])
+                    (start = DMRInfo[, 2], end = DMRInfo[, 3]),score=DMRInfo[, input5])
 
 annoData <- toGRanges(EnsDb.Hsapiens.v75)
 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
diff -r 0473a72c943c -r 8d05c398fecd chipeakanno_annopeaks.xml
--- a/chipeakanno_annopeaks.xml	Thu Jun 21 11:21:03 2018 -0400
+++ b/chipeakanno_annopeaks.xml	Thu Jun 21 11:38:08 2018 -0400
@@ -18,6 +18,8 @@
                     </param>
           <param name="input3" type="text" value="-5000" label="bindingRegionStart" help="e.g. to obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = startSite and bindingRegion = c(-5000, 3000)"/>
             <param name="input4" type="text" value="3000" label="bindingRegionEnd" help="e.g. to obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = nearestBiDirectionalPromoters and bindingRegion = c(-5000, 3000)"/>
+
+<param name="input5" type="text" value="1" label="Additional Column of Score" help="Position of Additional Column of the Score" />
     </inputs>
     <outputs>
         <data name="output1" format="txt" />