# HG changeset patch
# User testtool
# Date 1490008782 14400
# Node ID 741b192da59ccfe3478c47bbb4c52d483cf0c073
# Parent  6a9b9694acbf12080bb9202cab703476f8a61525
Uploaded

diff -r 6a9b9694acbf -r 741b192da59c annotate_peak/annotatePeak.R
--- a/annotate_peak/annotatePeak.R	Mon Mar 20 06:51:22 2017 -0400
+++ b/annotate_peak/annotatePeak.R	Mon Mar 20 07:19:42 2017 -0400
@@ -1,16 +1,22 @@
 require("ChIPseeker", quietly = TRUE)
 require("ChIPpeakAnno", quietly = TRUE)
 require("EnsDb.Hsapiens.v75", quietly = TRUE)
-require("data.table", quietly = TRUE)
+require("EnsDb.Mmusculus.v75", quietly = TRUE)
 
 options(warn = -1)
 options("download.file.method"="wget")
 
-args <- commandArgs(trailingOnly = TRUE)
+args <- commandArgs(trailingOnly = TRUE) 
 DMR = args[1]
-annoPeakTable = args[2]
+annoData = args[2]
+bindingType = args[3]
+upstream = as.numeric(args[4])
+downstream = as.numeric(args[5])
+ignore = args[6]
+annoPeakTable = args[7]
 
-DMRInfo = fread(
+#DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
   DMR,
   header = FALSE,
   sep = "\t",
@@ -22,9 +28,28 @@
                     ranges = IRanges
                     (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 
-annoData <- toGRanges(EnsDb.Hsapiens.v75)
+
+if (annoData == "human"){
+  annoData <- toGRanges(EnsDb.Hsapiens.v75)
+} else {
+  annoData <- toGRanges(EnsDb.Mmusculus.v75)
+}
 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
 
-anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
+if (ignore == "true"){
+  x <- TRUE
+} else {
+  x <- FALSE
+  }
+
 
-write.table(anno, annoPeakTable, row.names = FALSE)
\ No newline at end of file
+if (bindingType =="startSite"){
+anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("startSite"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
+} else if (bindingType =="endSite"){
+  anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("endSite"),  bindingRegion=c(upstream, downstream), ignore.peak.strand = x)  
+} else {
+  anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("fullRange"),  bindingRegion=c(upstream, downstream), ignore.peak.strand = x)  
+}
+  
+
+write.table(anno, annoPeakTable, row.names = FALSE)
diff -r 6a9b9694acbf -r 741b192da59c annotate_peak/annotatePeak.xml
--- a/annotate_peak/annotatePeak.xml	Mon Mar 20 06:51:22 2017 -0400
+++ b/annotate_peak/annotatePeak.xml	Mon Mar 20 07:19:42 2017 -0400
@@ -5,35 +5,35 @@
 <stdio>
    <exit_code range="1:" />
 </stdio>
-<command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData"  "$bindingType"  "$upstream" "$downstream" "$ignore.peak.strand" "$annoPeakTable"</command>
+<command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData"  "$bindingType"  "$upstream" "$downstream" "$ignore" "$annoPeakTable"</command>
   <inputs>
     <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
       <validator type="empty_field" message="This field is required."/>
     </param>
-    <param name="annoData" type="select" display="radio" label="annoData" help="choose your annoData human or mice">
+    <param name="annoData" type="select" label="annoData" help="choose your annoData human or mice">
       <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option>
       <option name="mice" type="float" value="">Mice</option>
     </param>
-    <param name="bindingType" type="select" display="radio" label="bindingType" help="choose bindingType">
+    <param name="bindingType" type="select" label="bindingType" help="choose bindingType">
       <option name="sS" type="text" value="startSite">startSite</option>
       <option name="eS" type="text" value="endSite">endSite</option>
       <option name="fR" type="text" value="fullRange">fullRange</option>
     </param>
-    <param name="ignore.peak.strand" type="select" display="radio" label="ignore.peak.strand" help="choose TRUE or FALSE">
+    <param name="ignore" type="select" label="ignore.peak.strand" help="choose TRUE or FALSE">
       <option name="T" type="text" value="TRUE">true</option>
       <option name="F" type="text" value="FALSE">false</option>
     </param>
-    <param name="upstream" type="float" value=""
+    <param name="upstream" type="text" value=""
 	       label="upstream - number no bigger than 0"
 	       help="e.g. '-5000'" >
       </param>
-      <param name="downstream" type="float" value=""
+      <param name="downstream" type="text" value=""
       	       label="downstream - number no less than 1"
       	       help="e.g. '5000'" >
             </param>
   </inputs>
   <outputs>
-    <data format="csv" name="annoPeakTable" label="peakAnno.csv"/>
+    <data format="txt" name="annoPeakTable" label="peakAnno.txt"/>
   </outputs>
   <tests>
     <test>
@@ -44,7 +44,7 @@
           </collection>
         </element>
         </param>
-        <output format="csv" name="annoPeakTable" label="test-data/annoPeakTable.csv"/>
+        <output format="txt" name="annoPeakTable" label="test-data/annoPeakTable.txt"/>
         </test>
     </tests>
   <help>
diff -r 6a9b9694acbf -r 741b192da59c annotate_peak/tool_dependencies.xml
--- a/annotate_peak/tool_dependencies.xml	Mon Mar 20 06:51:22 2017 -0400
+++ b/annotate_peak/tool_dependencies.xml	Mon Mar 20 07:19:42 2017 -0400
@@ -6,10 +6,11 @@
                         <package name="R" version="3.2.1" />
                       </repository>
 
-                      <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/ChIPseeker_1.10.3.tar.gz</package>
-                      <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/ChIPpeakAnno_3.8.9.tar.gz</package>
+                      <package>https://bioconductor.org/packages/release/bioc/src/contrib/ChIPseeker_1.10.3.tar.gz</package>
+                      <package>https://bioconductor.org/packages/release/bioc/src/contrib/ChIPpeakAnno_3.8.9.tar.gz</package>
                       <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.26.3.tar.gz</package>
                       <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz</package>
+                      <package>https://bioconductor.org/packages/release/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.1.0.tar.gz</package>
                       <package>http://bioconductor.org/packages/release/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.1.0.tar.gz</package>
 
                       <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">