Galaxy |

Changeset 0:f38763b52f33 (2014-07-28)

Next changeset 1:f0b6217f4a0c (2015-11-11)

Commit message:
Imported from capsule None

added:
lda_analy.xml
r_wrapper.sh
test-data/lda_analy_output.txt
test-data/matrix_generator_for_pc_and_lda_output.tabular
tool_dependencies.xml

diff -r 000000000000 -r f38763b52f33 lda_analy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lda_analy.xml Mon Jul 28 11:56:39 2014 -0400

[

b'@@ -0,0 +1,288 @@\n+<tool id="lda_analy1" name="Perform LDA" version="1.0.1">\n+\t<description>Linear Discriminant Analysis</description>\n+ <requirements>\n+ <requirement type="package" version="2.11.0">R</requirement>\n+ </requirements>\n+\t<command interpreter="sh">r_wrapper.sh $script_file</command>\n+\t<inputs>\n+\t\t<param format="tabular" name="input" type="data" label="Source file"/>\n+\t\t<param name="cond" size="30" type="integer" value="3" label="Number of principal components" help="See TIP below">\n+\t\t\t<validator type="empty_field" message="Enter a valid number of principal components, see syntax below for examples"/>\n+\t\t</param>\n+\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="txt" name="output" />\n+\t</outputs>\n+\n+\t<tests>\n+\t\t<test>\n+\t\t\t<param name="input" value="matrix_generator_for_pc_and_lda_output.tabular"/>\n+\t\t\t<output name="output" file="lda_analy_output.txt"/>\n+\t\t\t<param name="cond" value="2"/>\n+\n+\t\t</test>\n+\t</tests>\n+\n+\t<configfiles>\n+ \t<configfile name="script_file">\n+\n+ rm(list = objects() )\n+\n+ ############# FORMAT X DATA #########################\n+ format<-function(data) {\n+ ind=NULL\n+ for(i in 1 : ncol(data)){\n+ if (is.na(data[nrow(data),i])) {\n+ ind<-c(ind,i)\n+ }\n+ }\n+ #print(is.null(ind))\n+ if (!is.null(ind)) {\n+ data<-data[,-c(ind)]\n+ }\n+\n+ data\n+ }\n+\n+ ########GET RESPONSES ###############################\n+ get_resp<- function(data) {\n+ resp1<-as.vector(data[,ncol(data)])\n+ resp=numeric(length(resp1))\n+ for (i in 1:length(resp1)) {\n+ if (resp1[i]=="Y ") {\n+ resp[i] = 0\n+ }\n+ if (resp1[i]=="X ") {\n+ resp[i] = 1\n+ }\n+ }\n+ return(resp)\n+ }\n+\n+ ######## CHARS TO NUMBERS ###########################\n+ f_to_numbers<- function(F) { \n+ ind<-NULL\n+ G<-matrix(0,nrow(F), ncol(F))\n+ for (i in 1:nrow(F)) {\n+ for (j in 1:ncol(F)) {\n+ G[i,j]<-as.integer(F[i,j])\n+ }\n+ }\n+ return(G)\n+ }\n+\n+ ###################NORMALIZING#########################\n+ norm <- function(M, a=NULL, b=NULL) {\n+ C<-NULL\n+ ind<-NULL\n+\n+ for (i in 1: ncol(M)) {\n+ if (sd(M[,i])!=0) {\n+ M[,i]<-(M[,i]-mean(M[,i]))/sd(M[,i])\n+ }\n+ # else {print(mean(M[,i]))} \n+ }\n+ return(M)\n+ }\n+\n+ ##### LDA DIRECTIONS #################################\n+ lda_dec <- function(data, k){\n+ priors=numeric(k)\n+ grandmean<-numeric(ncol(data)-1)\n+ means=matrix(0,k,ncol(data)-1)\n+ B = matrix(0, ncol(data)-1, ncol(data)-1)\n+ N=nrow(data)\n+ for (i in 1:k){\n+ priors[i]=sum(data[,1]==i)/N\n+ grp=subset(data,data\\$group==i)\n+ means[i,]=mean(grp[,2:ncol(data)])\n+ #print(means[i,])\n+ #print(priors[i])\n+ #print(priors[i]*means[i,])\n+ grandmean = priors[i]*means[i,] + grandmean \n+ }\n+\n+ for (i in 1:k) {\n+ B= B + priors[i]*((means[i,]-grandmean)%*%t(means[i,]-grandmean))\n+ }\n+ \n+ W = var(data[,2:ncol(data)])\n+ svdW = svd(W)\n+ inv_sqrtW =solve(svdW\\$v %*% diag(sqrt(svdW\\$d)) %*% t(svdW\\$v))\n+ B_star= t(inv_sqrtW)%*%B%*%inv_sqrtW\n+ B_star_decomp = svd(B_star)\n+ directions = inv_sqrtW%*%B_star_decomp\\$v\n+ return( list(directions, B_star_decomp\\$d) ) \n+ }\n+\n+ ################ NAI'..b' # print(paste(c(msg, \'overall : \', (1-er)*100, "%."),collapse=" "))\n+ # print(paste(c(msg, \'within escapes : \', (1-er_esc)*100, "%."),collapse=" "))\n+ # print(paste(c(msg, \'within subjects: \', (1-er_subj)*100, "%."),collapse=" ")) \n+ }\n+ return(c((1-er)*100, (1-er_esc)*100, (1-er_subj)*100)) \n+ }\n+\n+ ## Main Function ##\n+\n+\tfiles<-matrix("${input}", 1,1, byrow=T)\n+\n+\td<-"${cond}" # Number of PC\n+\n+\ttau<-seq(0,1, by=0.005)\n+\t#tau<-seq(0,1, by=0.1)\n+\tfor_curve=matrix(-10, 3,length(tau))\n+\n+\t##############################################################\n+\n+\ttest_data_whole_X <-read.delim(files[1,1], row.names=1)\n+\n+\t#### FORMAT TRAINING DATA ####################################\n+\t# get only necessary columns \n+\n+\ttest_data_whole_X<-format(test_data_whole_X)\n+\toligo_labels<-test_data_whole_X[1:(nrow(test_data_whole_X)-1),ncol(test_data_whole_X)]\n+\ttest_data_whole_X<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)]\n+\n+\tX_names<-colnames(test_data_whole_X)[1:ncol(test_data_whole_X)]\n+\ttest_data_whole_X<-t(test_data_whole_X)\n+\tresp<-get_resp(test_data_whole_X) \n+\tldaqda_resp = resp + 1\n+\ta<-sum(resp)\t\t# Number of Subject\n+\tb<-length(resp) - a\t# Number of Escape \n+\t## FREQUENCIES #################################################\n+\tF<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)]\n+\tF<-f_to_numbers(F)\n+\tFN<-norm(F, a, b)\n+\tss<-svd(FN)\n+\teigvar<-NULL\n+\teig<-ss\\$d^2\n+\n+\tfor ( i in 1:length(ss\\$d)) {\n+\t\teigvar[i]<-sum(eig[1:i])/sum(eig)\n+\t}\n+\n+\t#print(paste(c("Variance explained : ", eigvar[d]*100, "%"), collapse=""))\n+\t\n+\tZ<-F%*%ss\\$v\n+\n+\tldaqda_data <- data.frame(group=ldaqda_resp,Z[,1:d])\n+\tlda_dir<-lda_dec(ldaqda_data,2)\n+\ttrain_lda_pred <-Z[,1:d]%*%lda_dir[[1]]\n+\n+\t############# NAIVE BAYES CROSS-VALIDATION #############\n+\t### LDA #####\n+\n+\ty<-ldaqda_resp\n+\tX<-F\n+\tcv<-matrix(c(rep(\'NA\',nrow(test_data_whole_X))), nrow(test_data_whole_X), length(tau))\n+\tfor (i in 1:nrow(test_data_whole_X)) {\n+\t#\tprint(i)\n+\t\tresp<-y[-i]\n+\t\tp<-matrix(X[-i,], dim(X)[1]-1, dim(X)[2])\n+\t\ttestdata<-matrix(X[i,],1,dim(X)[2])\n+\t\tp1<-norm(p)\n+\t\tsss<-svd(p1)\n+\t\tpred<-(p%*%sss\\$v)[,1:d]\n+\t\ttest<- (testdata%*%sss\\$v)[,1:d]\n+\t\tlda <- lda_dec(data.frame(group=resp,pred),2)\n+\t\tpred <- pred[,1:d]%*%lda[[1]][,1]\n+\t\ttest <- test%*%lda[[1]][,1]\n+\t\ttest<-matrix(test, 1, length(test))\n+\t\tfor (t in 1:length(tau)) {\n+\t\t\tcv[i, t] <- naive_bayes_classifier (resp, pred, test,k=2, tau[t]) \n+\t\t}\n+ \t}\n+\n+\tfor (t in 1:length(tau)) {\n+\t\ttr_err<-ext_error_rate(cv[,t], ldaqda_resp , c("CV"), 1)\n+\t\tfor_curve[1:3,t]<-tr_err\n+\t}\n+\n+\tdput(for_curve, file="${output}")\n+\n+\n+\t\t</configfile>\n+\t</configfiles>\n+\n+\t<help>\n+\n+.. class:: infomark\r\n+\r\n+**TIP:** If you want to perform Principal Component Analysis (PCA) on the give numeric input data (which corresponds to the "Source file First in "Generate A Matrix" tool), please use *Multivariate Analysis/Principal Component Analysis*\r\n+\r\n+-----\r\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+This tool consists of the module to perform the Linear Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873)\n+\n+*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment Predicts Expression Patterns on the Human \tInactive X Chromosome. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151*\n+\n+-----\n+\n+.. class:: warningmark\r\n+\r\n+**Note**\r\n+\n+- Output from "Generate A Matrix" tool is used as input file for this tool \r\n+- Output of this tool contains LDA classification success rates for different values of the turning parameter tau (from 0 to 1 with 0.005 interval). This output file will be used to establish the ROC plot, and you can obtain more detail information from this plot. \n+\n+\n+</help>\n+\n+</tool>\n'

diff -r 000000000000 -r f38763b52f33 r_wrapper.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_wrapper.sh Mon Jul 28 11:56:39 2014 -0400

@@ -0,0 +1,23 @@
+#!/bin/sh
+
+### Run R providing the R script in $1 as standard input and passing
+### the remaining arguments on the command line
+
+# Function that writes a message to stderr and exits
+fail()
+{
+ echo "$@" >&2
+ exit 1
+}
+
+# Ensure R executable is found
+which R > /dev/null || fail "'R' is required by this tool but was not found on path"
+
+# Extract first argument
+infile=$1; shift
+
+# Ensure the file exists
+test -f $infile || fail "R input file '$infile' does not exist"
+
+# Invoke R passing file named by first argument to stdin
+R --vanilla --slave $* < $infile

diff -r 000000000000 -r f38763b52f33 test-data/lda_analy_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lda_analy_output.txt Mon Jul 28 11:56:39 2014 -0400

b'@@ -0,0 +1,134 @@\n+structure(c(37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 40.2298850574713, 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43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 56.3218390804598, 78.1818181818182, 18.75), .Dim = c(3L, \n+201L))\n'

diff -r 000000000000 -r f38763b52f33 test-data/matrix_generator_for_pc_and_lda_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_output.tabular Mon Jul 28 11:56:39 2014 -0400

b'@@ -0,0 +1,88 @@\n+ \tAGTR2 \tARHGEF9 \tBRWD3 \tCLCN5 \tFMR1 \tGPC3 \tGPR173 \tGRIA3 \tGSPT2 \tHUWE1 \tKIAA2022 \tKLF8 \tMAGEH1 \tMTM1 \tNUDT10 \tNUDT11 \tPAGE1 \tPAGE4 \tPAK3 \tPCSK1N \tPGK1 \tPHF6 \tRRAGB \tSHROOM4 \tSOX3 \tTMEM29 \tTRO \tTSR2 \tUSP51 \tUXT \tZDHHC15 \tZDHHC9 \tX(SUM) \tAPOOL \tAR \tBEX4 \tBEX5 \tCHIC1 \tCHM \tCPXCR1 \tCSTF2 \tCXCR3 \tCXorf26 \tCYSLTR1 \tDACH2 \tDIAPH2 \tDRP2 \tEDA \tESX1 \tFGF16 \tFXYD8 \tGPR23 \tHDX \tHEPH \tIL1RAPL2 \tITM2A \tKIAA1166 \tKLHL4 \tLAS1L \tMAGEE1 \tMAGEE2 \tMSN \tMTMR8 \tNAP1L2 \tNRK \tNSBP1 \tNXF3 \tP2RY10 \tPABPC5 \tPOF1B \tRNF12 \tRPS6KA6 \tSLC7A3 \tSPIN2A \tSPIN3 \tSPIN4 \tSTARD8 \tSYTL4 \tTAF9B \tTBX22 \tTCEAL2 \tTCEAL4 \tTMEM28 \tUBQLN2 \tUPRT \tZCCHC5 \tZNF711 \tZXDA \tY(SUM) \t\n+CTCAGAAAAAAA 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\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\tEOL\n+GTCAGATGGATA \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t10\tEOL\n+TCATCTGACAAAGGGCTAATATCCAG \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\tEOL\n+TTTGTCAGGTTTGTCAAAG \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tEOL\n+TTCTTAATCCAGTCTATCATT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t1\t0\t0\t0\t1\t0\t1\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t3\t0\t0\t15\tEOL\n+TTTAATCCATCTTGA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t1\t0\t0\t3\t1\t0\t0\t0\t3\t0\t0\t1\t0\t0\t0\t0\t3\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t4\t0\t0\t20\tEOL\n+AAACTACCATCAGAGTGAACAGGCA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t1\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t8\tEOL\n+GCCATCAGAGAAAT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t8\tEOL\n+ACAGGCAACCTACA \t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t4\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t7\tEOL\n+GCAACCTACTCA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\tEOL\n+TAGAAAACCCCAT \t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t2\t0\t0\t8\tEOL\n+ \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \t \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \t \t\n'

diff -r 000000000000 -r f38763b52f33 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jul 28 11:56:39 2014 -0400

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="2.11.0">
+        <repository changeset_revision="5824d2b3bc8b" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>