# HG changeset patch
# User testtool
# Date 1486396715 18000
# Node ID 88964c4b12a01182cd45127e0d5982ea007ef093

Uploaded

diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/._.DS_Store
Binary file annoPeakFigure/._.DS_Store has changed
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/._annoPeakFigure.png
Binary file annoPeakFigure/._annoPeakFigure.png has changed
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/annoPeakFigure.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/annoPeakFigure.R	Mon Feb 06 10:58:35 2017 -0500
@@ -0,0 +1,33 @@
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+
+options(warn = -1)
+
+args <- commandArgs(trailingOnly = TRUE)
+DMR = args[1]
+annoPeakFigure = args[2]
+
+#DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
+  DMR,
+  header = FALSE,
+  sep = "\t",
+  stringsAsFactors = FALSE,
+  quote = ""
+)
+
+DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+                    ranges = IRanges
+                    (start = DMRInfo[, 2], end = DMRInfo[, 3]))
+
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+
+#annoPeakFigure <- ('test-data/annoPeakFigure.png')
+
+png(file = annoPeakFigure,
+    width = 1200,
+    height = 600)
+
+upsetplot(annotatePeak, vennpie = TRUE)
+
+dev.off()
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/annoPeakFigure.png
Binary file annoPeakFigure/annoPeakFigure.png has changed
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/annoPeakFigure.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/annoPeakFigure.xml	Mon Feb 06 10:58:35 2017 -0500
@@ -0,0 +1,35 @@
+<tool id="APfigure" name="annoPeakFigure" version="1.16.2">
+  <requirements>
+         <requirement type="package" version="3.2.1">R</requirement>
+     </requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <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="annoPeakFigure" label="annoPeakFigure.png"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+          <element name="DMR" value="test-data/DMR.bed"/>
+          </collection>
+        </element>
+        </param>
+        <output format="png" name="annoPeakFigure" label="test-data/annoPeakFigure.png"/>
+        </test>
+    </tests>
+  <help>
+**Description**
+</help>
+<citations>
+DMR
+</citations>
+</tool>
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/test-data/._.DS_Store
Binary file annoPeakFigure/test-data/._.DS_Store has changed
diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/test-data/DMR.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/test-data/DMR.bed	Mon Feb 06 10:58:35 2017 -0500
@@ -0,0 +1,9881 @@
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diff -r 000000000000 -r 88964c4b12a0 annoPeakFigure/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/tool_dependencies.xml	Mon Feb 06 10:58:35 2017 -0500
@@ -0,0 +1,279 @@
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+                          https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz
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+                      <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">
+                          https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz
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+                      <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">
+                          https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz
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+                      <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">
+                          https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz
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+                  </action>
+              </actions>
+          <readme>
+          </readme>
+  </tool_dependency>