# HG changeset patch
# User testtool
# Date 1489748929 14400
# Node ID 6bcf1f0bff41f9dcde2659f95cc58340de911260
# Parent  a23d604eb17b7338cbdbcb37974d89f0cf1b1d8c
Uploaded

diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/.Rapp.history
diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/.Rhistory
--- a/annoPeakFigure/.Rhistory	Tue Feb 28 05:55:29 2017 -0500
+++ b/annoPeakFigure/.Rhistory	Fri Mar 17 07:08:49 2017 -0400
@@ -263,3 +263,4 @@
 upsetplot(annotatePeak, vennpie = TRUE)
 dev.off()
 getwd()
+??GRanges
diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/annoPeakFigure.R
--- a/annoPeakFigure/annoPeakFigure.R	Tue Feb 28 05:55:29 2017 -0500
+++ b/annoPeakFigure/annoPeakFigure.R	Fri Mar 17 07:08:49 2017 -0400
@@ -1,9 +1,13 @@
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+require("EnsDb.Hsapiens.v75", quietly = TRUE)
+
 options(warn = -1)
+options("download.file.method"="wget")
 
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
-annoPeakFigure1 = args[2]
-annoPeakFigure2 = args[3]
+annoPeakTable = args[2]
 
 #DMR <- ("test-data/DMR.bed")
 DMRInfo = read.table(
@@ -14,28 +18,22 @@
   quote = ""
 )
 
-DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
-                    ranges = IRanges
-                    (start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- GRanges(seqnames = DMRInfo[, 1],
+                 ranges = IRanges
+                 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 
-annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annoData <- toGRanges(EnsDb.Hsapiens.v75)
+seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
 
-#annoPeakFigure1 <- ('test-data/annoPeakUpset.png')
-#annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png')
+anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
 
-png(file = annoPeakFigure1,
+#annoPeakFigure <- ('test-data/annoPie.png')
+
+png(file = annoPeakFigure,
     width = 1200,
     height = 600)
 
-plotAnnoBar(annotatePeak)
+pie1(table(anno$insideFeature))
 
 dev.off()
 
-png(file = annoPeakFigure2,
-    width = 1200,
-    height = 600)
-
-upsetplot(annotatePeak, vennpie = TRUE)
-
-dev.off()
-
diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/annoPeakFigure.xml
--- a/annoPeakFigure/annoPeakFigure.xml	Tue Feb 28 05:55:29 2017 -0500
+++ b/annoPeakFigure/annoPeakFigure.xml	Fri Mar 17 07:08:49 2017 -0400
@@ -1,19 +1,18 @@
 <tool id="APfigure" name="annoPeakFigure" version="1.16.2">
   <requirements>
-         <requirement type="package" version="3.2.1">R</requirement>
-     </requirements>
+   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
+</requirements>
 <stdio>
    <exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure1" "$annoPeakFigure2"</command>
+  <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure"</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>
   </inputs>
   <outputs>
-    <data format="png" name="annoPeakFigure1" label="annoPeakUpset.png"/>
-    <data format="png" name="annoPeakFigure2" label="annoPeakAnnoBar.png"/>
+    <data format="png" name="annoPeakFigure" label="annoPeakFigure.png"/>
   </outputs>
   <tests>
     <test>
@@ -24,8 +23,7 @@
           </collection>
         </element>
         </param>
-        <output format="png" name="annoPeakFigure" label="test-data/annoPeakUpset.png"/>
-        <output format="png" name="annoPeakFigure" label="test-data/annoPeakAnnoBar.png"/>
+        <output format="png" name="annoPeakFigure" label="test-data/annoPeakFigure.png"/>
         </test>
     </tests>
   <help>
diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/tool_dependencies 10.27.23.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/tool_dependencies 10.27.23.xml	Fri Mar 17 07:08:49 2017 -0400
@@ -0,0 +1,276 @@
+<?xml version='1.0' encoding='utf-8'?>
+  <tool_dependency>
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <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/GenomicRanges_1.26.3.tar.gz</package>
+                      <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz</package>
+
+                      <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">
+                          https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz
+                      </package>
+                      <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">
+                          https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz
+                      </package>
+                      <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">
+                          https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz
+                      </package>
+                      <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">
+                          https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz
+                      </package>
+                      <package sha256sum="7f1aa58085a030b7855a4e189bea2f17ff72333a1f884f0ab7f5af1fbe101397">
+                          https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz
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+                      <package sha256sum="f9e132c35d3af919cff291465d030817ff74e56eb6b2770390ae8566881b62ed">
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diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/tool_dependencies.xml
--- a/annoPeakFigure/tool_dependencies.xml	Tue Feb 28 05:55:29 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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