# HG changeset patch
# User jiechenable1987
# Date 1330123336 18000
# Node ID 8933ecfb6ab28a1edcbc2e739100fed68d8a1dd2
Uploaded
diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/.hg_archival.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/.hg_archival.txt Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,5 @@
+repo: 55561a945415eba8ee6e8ad81a0d6f68bd91b873
+node: 55561a945415eba8ee6e8ad81a0d6f68bd91b873
+branch: default
+latesttag: null
+latesttagdistance: 1
diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.R Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,48 @@
+#! /soft/general/R-2.13.0/bin/Rscript
+rm(list=ls(all=TRUE))
+
+########################################################################
+# HumMeth27QCReport.R a parser of the HumMeth27QCReport R package
+# Copyright (C) 2011 Andreu Alibes (aalibes@gmail.com)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see .
+########################################################################
+
+
+
+##First read in the arguments listed at the command line
+args=(commandArgs(TRUE))
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+if(length(args)==0){
+ print("No arguments supplied.")
+ ##supply default values
+ Directory = ""
+ Plat = ""
+ pvalue = ""
+ chrom = ""
+ method = ""
+} else {
+# print(args)
+ for(i in 1:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+}
+
+library("HumMeth27QCReport")
+Dir <- Directory
+ImportDataR <- ImportData(Dir)
+normMvalues <- HumMeth27QCReport(ImportDataR, platform = Plat, pval = pvalue, ChrX = chrom, ClustMeth=method)
diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.py Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,86 @@
+# Based on rgQC.py by ross lazarus (Version from 20100914)
+
+########################################################################
+# HumMeth27QCReport.py a parser of the HumMeth27QCReport R package
+# Copyright (C) 2011 Andreu Alibes (aalibes@gmail.com)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see .
+########################################################################
+from optparse import OptionParser
+import os, sys
+
+if __name__ == "__main__":
+ u = """ called in xml as
+
+ HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX'
+-1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path'
+
+
+ """
+ progname = os.path.basename(sys.argv[0])
+ if len(sys.argv) < 14:
+ print '%s requires at least 14 parameters - got %d = %s' % (progname,len(sys.argv),sys.argv)
+ sys.exit(1)
+ parser = OptionParser(usage=u, version="%prog 0.01")
+ a = parser.add_option
+ a("-a","--avefile",dest="avefile")
+ a("-c","--ctrfile",dest="ctrfile")
+ a("-s","--smplfile",dest="smplfile")
+ a("-d","--discfile",dest="discfile")
+ a("-l","--platf",dest="platf")
+ a("-v","--pval",dest="pval")
+ a("-m","--clustmethd",dest="clustmethd")
+ a("-x","--chrx",dest="chrx")
+ a("-1","--oQualityCheck",dest="oQualityCheck")
+ a("-2","--oSample",dest="oSample")
+ a("-3","--oInternalControl",dest="oInternalControl")
+ a("-4","--oExplorativeAnalysis",dest="oExplorativeAnalysis")
+ a("-5","--oNormalizedMvalues",dest="oNormalizedMvalues")
+ a("-6","--oQC_Analysis",dest="oQC_Analysis")
+ a("-p","--patho",dest="newfpath")
+
+ (options,args) = parser.parse_args()
+ avefile = options.avefile
+ ctrfile = options.ctrfile
+ smplfile = options.smplfile
+ discfile = options.discfile
+ platf = options.platf
+ pval = options.pval
+ clustmethd = options.clustmethd
+ chrx = options.chrx
+ oQualityCheck = options.oQualityCheck
+ oSample = options.oSample
+ oInternalControl = options.oInternalControl
+ oExplorativeAnalysis = options.oExplorativeAnalysis
+ oNormalizedMvalues = options.oNormalizedMvalues
+ oQC_Analysis = options.oQC_Analysis
+
+ newfpath = options.newfpath
+ newfpath = os.path.realpath(newfpath)
+ try:
+ os.makedirs(newfpath)
+ except:
+ pass
+ try:
+ os.system("cp " + avefile + " " + newfpath+"/AvgBeta.txt")
+ os.system("cp " + ctrfile + " " + newfpath+"/Control.txt")
+ os.system("cp " + smplfile + " " + newfpath+"/Sample.txt")
+ if(discfile != 'None'):
+ os.system("cp " + discfile + " " + newfpath+"/Discard.txt")
+
+ execstring = "/data/apache/galaxy.test.crg/htdocs/galaxy-dist/tools/CRG-Tools/HumMeth27QCReport.R \"Directory=\'"+newfpath+"\'\" \"Plat=\'"+platf+"\'\" \"pvalue=\'"+pval+"\'\" \"chrom=\'"+chrx+"\'\" \"method=\'"+clustmethd+"\'\""
+ os.system(execstring + " 2> /dev/null")
+ os.system("cd " + newfpath + "; mv Sample.pdf " + oSample + "; mv InternalControl.pdf " + oInternalControl + ";mv QualityCheck.pdf " + oQualityCheck + ";mv ExplorativeAnalysis.pdf " + oExplorativeAnalysis + ";mv NormalizedMvalues.txt " + oNormalizedMvalues + ";mv QC_Analysis.xls " + oQC_Analysis )
+ except:
+ pass
diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.xml Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,64 @@
+
+ Quality Control for a methylation array
+
+ HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX' -1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path'
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+This tool is a Quality Control for Illumina Infinium methylation arrays. It uses an R package (HumMeth27QCReport) created by
+Francesco Mancuso and Guglielmo Roma from the Bioinformatics core at the Center for Genomic Regulation in Barcelona.
+Help: http://biocore.crg.cat/wiki/HumMeth27QCReport and francesco.mancuso@crg.eu
+
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diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.xml~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.xml~ Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,64 @@
+
+ Quality Control for a methylation array
+
+ HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX' -1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path'
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+This tool is a Quality Control for Illumina Infinium methylation arrays. It uses an R package (HumMeth27QCReport) created by
+Francesco Mancuso and Guglielmo Roma from the Bioinformatics core at the Center for Genomic Regulation in Barcelona.
+Help: http://biocore.crg.cat/wiki/HumMeth27QCReport and francesco.mancuso@crg.eu
+
+
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diff -r 000000000000 -r 8933ecfb6ab2 qcma-55561a945415/HumMeth27QCReport/README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/README.txt Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,8 @@
+HumMeth27QCReport is a tool for quality control and preprocessing of Illumina's Infinium BeadChip methylation assays. The automated analysis pipeline comprises data import, normalization, quality diagnostics and data export.
+
+This requires:
+
+* Perl
+* Python 2
+* R (≥ 2.13.0)
+* The following R packages: methylumi, lumi, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, amap, Hmisc, gplots, plotrix, WriteXLS, tcltk2, AnnotationDbi (≥ 0.0.89), Biobase (≥ 1.15.29)