| Next changeset 1:6278004aa9b2 (2017-02-28) |
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Commit message:
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added:
annoPeakFigure/._.DS_Store annoPeakFigure/._annoPeakFigure.png annoPeakFigure/annoPeakFigure.R annoPeakFigure/annoPeakFigure.png annoPeakFigure/annoPeakFigure.xml annoPeakFigure/test-data/._.DS_Store annoPeakFigure/test-data/DMR.bed annoPeakFigure/tool_dependencies.xml |
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| 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 |
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| @@ -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() |
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| 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 |
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| @@ -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> |
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| 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 |
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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 |
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| b'@@ -0,0 +1,279 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+ <tool_dependency>\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1" />\n+ </repository>\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n+ https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n+ </package>\n+ <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n+ https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n+ </package>\n+ <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n+ https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n+ 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