| Next changeset 1:18e59d049951 (2016-03-18) |
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frequency_sliding/._.DS_Store frequency_sliding/._eqtl_genes_polygon_plot.txt frequency_sliding/._frequency_sliding.py frequency_sliding/._frequency_sliding.xml frequency_sliding/._readme.txt frequency_sliding/eqtl_genes_polygon_plot.txt frequency_sliding/frequency_sliding.py frequency_sliding/frequency_sliding.xml frequency_sliding/readme.txt frequency_sliding/test-data/._.DS_Store frequency_sliding/test-data/input/._.DS_Store frequency_sliding/test-data/input/._chr_summary.txt frequency_sliding/test-data/input/._frequency.txt frequency_sliding/test-data/input/._frequency_summary.txt frequency_sliding/test-data/input/chr_summary.txt frequency_sliding/test-data/input/frequency.txt frequency_sliding/test-data/input/frequency_summary.txt frequency_sliding/test-data/output/._.DS_Store frequency_sliding/test-data/output/._polygon_plot.pdf frequency_sliding/test-data/output/._sliding_frequency.txt frequency_sliding/test-data/output/._sliding_lookup.txt frequency_sliding/test-data/output/polygon_plot.pdf frequency_sliding/test-data/output/sliding_frequency.txt frequency_sliding/test-data/output/sliding_lookup.txt frequency_sliding/tool_dependencies.xml |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/eqtl_genes_polygon_plot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/eqtl_genes_polygon_plot.txt Fri Mar 18 05:22:30 2016 -0400 |
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| @@ -0,0 +1,43 @@ +# polygon eqtl + genes plots + +#setwd("/Users/nanettecoetzer/Documents/Bioinformatics/MAIZE_project/eQTL_pipeline/April_2012_pipeline_scripts/July_2012") +data <- read.table("sliding_frequency.txt",sep="\t",header=TRUE) +num.chr = max(data[,2]) + + +pdf(paste("Rplot_eQTL_genes_polygon.pdf",sep=""),width=20,height=12) +if (num.chr <= 6) { + par(mfrow=c(2,3)) + } +if (num.chr>6 & num.chr<=9) { + par(mfrow=c(3,3)) + } +if (num.chr>9 & num.chr<=12) { + par(mfrow=c(3,4)) + } +if (num.chr>12 & num.chr<=15) { + par(mfrow=c(3,5)) + } +if (num.chr>15 & num.chr<=20) { + par(mfrow=c(4,5)) + } + +len_trans <- length(data[,6]) +max_trans <- sort(data[,6])[len_trans-3] + +for (k in 1:num.chr) { + bin1 <- data[data[,2]==k,1] + bin <- c(1:length(bin1)) + cis <- data[data[,2]==k,5] + trans <- data[data[,2]==k,6] + genes <- data[data[,2]==k,7] + m = max(trans) + + plot(bin,trans, ylim=c(0, max_trans), type="n",col="red", lwd=1, ylab="Frequency",main=paste("Chr ",k),xlab="Sliding window bins") + polygon(c(0,genes,0),col="green",border="green") + polygon(c(0,trans,0),col="red",border="red") + polygon(c(0,cis,0),col="blue",border="blue") + x <- 2.2*(max(bin)/3) + legend(x,max_trans,c("genes","trans","cis"),col=c("green","red","blue"),lty=1,lwd=2) + } +dev.off() \ No newline at end of file |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/frequency_sliding.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/frequency_sliding.py Fri Mar 18 05:22:30 2016 -0400 |
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| b'@@ -0,0 +1,345 @@\n+"""\n+@summary: Calculate the frequency of eQTLs and genes per sliding window bin\n+@author: nanette.coetzer@gmail.com\n+@version 5\n+\n+"""\n+import optparse, sys\n+import subprocess\n+import tempfile\n+import os, re\n+\n+def stop_err( msg ):\n+ sys.stderr.write( "%s\\n" % msg )\n+ sys.exit()\n+ \n+def __main__():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option("-m", "--rscript", default=None, dest="rscript", \n+ help="R script")\n+ parser.add_option("-i", "--input1", default=None, dest="input1", \n+ help="Frequency per bin file")\n+ parser.add_option("-j", "--input2", default=None, dest="input2", \n+ help="Lookup summary file")\n+ parser.add_option("-k", "--input3", default=None, dest="input3", \n+ help="Frequency summary file")\n+ parser.add_option("-o", "--output1", default=None, dest="output1", \n+ help="Sliding frequency file")\n+ parser.add_option("-p", "--output2", default=None, dest="output2", \n+ help="Sliding lookup file")\n+ parser.add_option("-q", "--output3", default=None, dest="output3", \n+ help="eQTL and genes polygon plot")\n+ (options, args) = parser.parse_args()\n+ \n+ try:\n+ open(options.input1, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the Lookup frequency file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the Lookup frequency file:\\n" + str(e))\n+ \n+ try:\n+ open(options.input2, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the Lookup summary file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the Lookup summary file:\\n" + str(e))\n+ \n+ try:\n+ open(options.input3, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the Frequency summary file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the Frequency summary file:\\n" + str(e))\n+ \n+ ##############################################\n+ ##############################################\n+\n+ infile3 = open(options.input3,\'r\') # Frequency summary file\n+ for line in infile3:\n+ if line.startswith("Number"):\n+ num_intervals = int(line.strip().split("\\t")[1])\n+ #print num_intervals\n+ infile3.close()\n+ \n+ chr_second_last = []\n+ chr_end = []\n+ tot = 0\n+ infile2 = open(options.input2,\'r\') # Lookup summary file\n+ for line in infile2:\n+ l = line.strip().split("\\t")\n+ if not l[4].startswith("i"):\n+ tot += int(l[4])\n+ chr_second_last.append(tot-2)\n+ chr_end.append(tot)\n+ \n+ freq_dict = {}\n+ sliding_id = 0\n+ prev_size = 0\n+ idlist = []\n+ slidingdict = {}\n+ cur_size = 0\n+ add_last = 0\n+ i = 0\n+ sizelist = []\n+ \n+ infile1 = open(options.input1,\'r\') # Frequency.txt\n+ \n+ # 1b is where an interval always starts with a 2cM bin (plus a small bin if available) --> never split 2 bins on either sides of a marker\n+ if num_intervals == 1:\n+ for line in infile1:\n+ l2 = line.strip().split("\\t")\n+ if not l2[0].startswith("int"):\n+ i += 1\n+ freq_dict[l2[0]] = l2\n+ if prev_size == 0:\n+ # end of chromosome\n+ if int(l2[0]) in chr_end:\n+ pass\n+ else:\n+ prev_size = float(l2[6])\n+ idlist.append(int(l2[0]))\n+ sizelist.append(float(l2[6]))\n+ cur_size = float(l2[6])\n+ add_last = 0\n+ else:\n+ prev_size = float(l2[6])\n+ \n+ if prev_size < 2 and add_last == 0:\n+ cur_size = float(cur_size) +'..b' float(cur_size) >= 6 and add_last == 0:\n+ sliding_id = sliding_id + 1\n+ slidingdict[int(sliding_id)] = idlist\n+ prev_size = float(l2[6])\n+ newsizelist = []\n+ newidlist = []\n+ newstart = 0\n+ c = 0\n+ cur_size = 0\n+ for s in range(len(sizelist)):\n+ if newstart == 1:\n+ newsizelist.append(sizelist[s])\n+ newidlist.append(idlist[s])\n+ cur_size += float(sizelist[s])\n+ if sizelist[s] == 2.0 and newstart == 0:\n+ c += 1\n+ if c == 2:\n+ newsizelist.append(sizelist[s])\n+ newidlist.append(idlist[s])\n+ cur_size += float(sizelist[s])\n+ newstart = 1\n+ idlist = newidlist\n+ sizelist = newsizelist\n+ \n+ out1 = open(options.output1,\'w\') # Frequency.txt\n+ out2 = open(options.output2,\'w\') \n+ #out1.write("sliding.id\\tchr\\tsliding.cM\\tsliding.eQTL\\tsliding.cis.eQTL\\tsliding.trans.eQTL\\tsliding.genes\\tsliding.eQTL/cM\\tsliding.eQTL/cM/10genes\\n")\n+ out1.write("sliding.id\\tchr\\tsliding.cM\\tsliding.all.eQTL\\tsliding.cis.eQTL\\tsliding.trans.eQTL\\tsliding.genes\\tsliding.all.eQTL/cM\\tsliding.cis.eQTL/cM\\tsliding.trans.eQTL/cM\\tsliding.genes/cM\\n")\n+ tcM = 0\n+ tEQTL = 0\n+ tGENES = 0\n+ \n+ for j in range(len(slidingdict.keys())):\n+ totcM = 0\n+ toteqtl = 0\n+ totcis = 0\n+ tottrans = 0\n+ totgenes = 0\n+ totEcM_all = 0\n+ totEcM_cis = 0\n+ totEcM_trans = 0\n+ totGcM = 0\n+ #totEcM10G = 0\n+ out2.write(str(j+1)+"\\t"+str(slidingdict[j+1])+"\\n")\n+ for k in slidingdict[j+1]:\n+ totcM += float(freq_dict[str(k)][6])\n+ toteqtl += float(freq_dict[str(k)][7])\n+ totcis += float(freq_dict[str(k)][8])\n+ tottrans += float(freq_dict[str(k)][9])\n+ totgenes += float(freq_dict[str(k)][10])\n+ \n+ chr = freq_dict[str(k)][1]\n+ if totgenes == 0:\n+ totgenes = 1\n+\n+ totEcM_all += round((toteqtl/totcM),2)\n+ totEcM_cis += round((totcis/totcM),2)\n+ totEcM_trans += round((tottrans/totcM),2)\n+ totGcM += round((totgenes/totcM),2)\n+ out1.write(str(j+1)+"\\t"+str(chr)+"\\t"+str(totcM)+"\\t"+str(toteqtl)+"\\t"+str(totcis)+"\\t"+str(tottrans)+"\\t"+str(totgenes)+"\\t"+str(totEcM_all)+"\\t"+str(totEcM_cis)+"\\t"+str(totEcM_trans)+"\\t"+str(totGcM)+"\\n")\n+ \n+ out1.close()\n+ infile1.close()\n+ infile2.close()\n+ out2.close()\n+ \n+\n+ # Create temp direcotry\n+ tempdir = tempfile.mkdtemp()\n+\n+ # copy INPUT file to the temp directory\n+ s = "cp %s %s/sliding_frequency.txt" %(options.output1, tempdir)\n+ subprocess.call(s, shell=True)\n+\n+ # create R script => save in temp directory\n+ # generate new header \n+ new_script = open(tempdir+"/new_script.r","w")\n+ header = "setwd(\\"%s\\")" %tempdir\n+ new_script.write(header+"\\n")\n+ # add script body\n+ script = open(options.rscript,"r")\n+ for line in script:\n+ new_script.write(line.strip()+"\\n")\n+ new_script.close()\n+ \n+ # run R script from temp directory\n+ s = "R CMD BATCH %s/new_script.r out.txt" %tempdir\n+ subprocess.call(s, shell=True)\n+ \n+ # run R script from temp directory\n+ s = "R CMD BATCH %s/new_script.r out.txt" %tempdir\n+ subprocess.call(s, shell=True)\n+ \n+ os.system("mv %s/Rplot_eQTL_genes_polygon.pdf %s" %(tempdir,options.output3))\n+ \n+ ##############################################\n+ \n+if __name__=="__main__": \n+ __main__()\n' |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/frequency_sliding.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/frequency_sliding.xml Fri Mar 18 05:22:30 2016 -0400 |
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| @@ -0,0 +1,132 @@ +<tool id="sliding_frequency5" name="Sliding Window frequency" version="5.0.0"> + <description>of eQTLs and genes</description> + <command interpreter="python"> + frequency_sliding.py --rscript \$R_SCRIPT_PATH/frequency_sliding/eqtl_genes_polygon_plot.txt --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 --output2 $output2 --output3 $output3 + </command> + <inputs> + <param label="Frequency per bin file" name="input1" type="data" format="tabular" help="A tabular file with eQTL and gene frequencies for each interval."></param> + <param label="Lookup summary file" name="input2" type="data" format="tabular" help="A tabular file number of cM, bp, inteval positions and bins on each chromosome."></param> + <param label="Frequency summary file" name="input3" type="data" format="tabular" help="A tabular file with the total number of genes, eQTLs, cM and number of permutations."></param> + </inputs> + <outputs> + <data format="tabular" name="output1" /> + <data format="tabular" name="output2" /> + <data format="pdf" name="output3" /> + </outputs> + <requirements> + <requirement type="set_environment">R_SCRIPT_PATH</requirement> + </requirements> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach. + +For 2 cM lookup bins: + +* For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals. + +Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals). + +Calculate the number of genes per sliding window (4 - 5.9 cM intervals). + +* For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals. + +Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals). + +Calculate the number of genes per sliding window (6 - 7.9 cM intervals). + +------- + +**Example input files** + +Frequency per bin file: frequency of all, cis and trans eQTLs and genes, each row correspond to a 2cM (or smaller) interval (11 columns; only a part of the file is shown):: + + int.id chr marker interval cM bp length_cM num.eQTL.all num.eQTL.cis num.eQTL.trans num.genes + 1 1 1 0.0001 0.0 2038278 2.0 94.0 2.0 64.0 12.0 + 2 1 1 0.0201 2.0 2466324 2.0 17.0 3.0 11.0 34.0 + 3 1 1 0.0401 4.0 2894370 2.0 8.0 2.0 5.0 29.0 + 4 1 1 0.0601 6.0 3322416 1.53 11.0 5.0 3.0 10.0 + 5 1 2 0.0754 7.53 3649871 2.0 27.0 6.0 19.0 18.0 + 6 1 2 0.0954 9.53 4095673 2.0 8.0 4.0 3.0 12.0 + 7 1 2 0.1154 11.53 4541476 2.0 4.0 2.0 2.0 17.0 + 8 1 2 0.1354 13.53 4987278 2.0 8.0 4.0 2.0 19.0 + 9 1 2 0.1554 15.53 5433081 2.0 5.0 0 3.0 15.0 + + +Chromosome summary file, each row correspond to a chromosome (6 columns; only a part of the file is shown). The last row gives the total across the genome:: + + chr markers cM bp int_positions bins + 1 27 324.4 301354135 177 176 + 2 14 169.11 237068873 92 91 + 3 19 221.29 232140174 123 122 + 4 20 188.37 241473504 105 104 + 5 20 203.82 217872852 110 109 + 6 17 195.85 169174353 106 105 + Total 117 1302.84 1399083891 713 707 + + +Frequency summary file (2 columns):: + + Total number of eQTLs (all) 31549 + Total number of cis-eQTLs 4863 + Total number of trans-eQTLs 21428 + Total number of genes 31036 + Total number of cM 1861.57 + Expected number of eQTL per cM (all) 16.95 + Expected number of cis-eQTL per cM 2.61 + Expected number of trans-eQTL per cM 11.51 + Expected number of genes per cM 16.67 + User specified number of permutations 1000 + Number of intervals per sliding window 2 + +------- + +**Example output files** + + +Sliding frequency file: Frequency of eQTLs and genes per sliding window interval (4 - 5.9 cM) output file, each row correspond to a sliding window interval (11 columns; only a part of the file is shown):: + + sliding.id chr sliding.cM sliding.all.eQTL sliding.cis.eQTL sliding.trans.eQTL sliding.genes sliding.all.eQTL/cM sliding.cis.eQTL/cM sliding.trans.eQTL/cM sliding.genes/cM + 1 1 4.0 111.0 5.0 75.0 46.0 27.75 1.25 18.75 11.5 + 2 1 4.0 25.0 5.0 16.0 63.0 6.25 1.25 4.0 15.75 + 3 1 5.53 46.0 13.0 27.0 57.0 8.32 2.35 4.88 10.31 + 4 1 4.0 35.0 10.0 22.0 30.0 8.75 2.5 5.5 7.5 + 5 1 4.0 12.0 6.0 5.0 29.0 3.0 1.5 1.25 7.25 + 6 1 4.0 12.0 6.0 4.0 36.0 3.0 1.5 1.0 9.0 + 7 1 4.0 13.0 4.0 5.0 34.0 3.25 1.0 1.25 8.5 + 8 1 5.24 67.0 5.0 46.0 41.0 12.79 0.95 8.78 7.82 + 9 1 4.0 57.0 5.0 39.0 53.0 14.25 1.25 9.75 13.25 + 10 1 4.0 13.0 3.0 9.0 58.0 3.25 0.75 2.25 14.5 + 11 1 4.0 11.0 3.0 5.0 54.0 2.75 0.75 1.25 13.5 + 12 1 4.0 11.0 4.0 3.0 35.0 2.75 1.0 0.75 8.75 + +Map sliding window IDs (first column) to lookup table IDs (second column) (2 columns; only a part of the file is shown):: + + 1 [1, 2] + 2 [2, 3] + 3 [3, 4, 5] + 4 [5, 6] + 5 [6, 7] + 6 [7, 8] + 7 [8, 9] + 8 [9, 10, 11] + 9 [11, 12] + 10 [12, 13] + 11 [13, 14] + 12 [14, 15] + 13 [15, 16] + 14 [16, 17] + 15 [17, 18] + 16 [18, 19] + 17 [19, 20, 21] + +Frequency per cM plot of cis-eQTL, trans-eQTL and genes (in pdf format, produced using R). + + + </help> +</tool> |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/readme.txt Fri Mar 18 05:22:30 2016 -0400 |
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| @@ -0,0 +1,32 @@ +====================================================================== +frequency_sliding +====================================================================== +### This is the fourth tool in the eQTL backend pipeline: +lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment + +Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2 + +Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach. + +For 2 cM lookup bins: + +* For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals. +Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals). +Calculate the number of genes per sliding window (4 - 5.9 cM intervals). + +* For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals. +Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals). +Calculate the number of genes per sliding window (6 - 7.9 cM intervals). + + +--------------- +Installation +--------------- + +The eQTL backend pipeline is available for: +* command line usage +* integration into Galaxy servers + + +Requirements: Python 2.7 + R 3.1.1 \ No newline at end of file |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/input/chr_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/test-data/input/chr_summary.txt Fri Mar 18 05:22:30 2016 -0400 |
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| @@ -0,0 +1,12 @@ +chr markers cM bp interval positions bins +1 27 324.4 301354135 177 176 +2 14 169.11 237068873 92 91 +3 19 221.29 232140174 123 122 +4 20 188.37 241473504 105 104 +5 20 203.82 217872852 110 109 +6 17 195.85 169174353 106 105 +7 12 111.16 176764762 63 62 +8 14 141.31 175793759 77 76 +9 11 158.78 156750706 85 84 +10 13 147.48 150189435 81 80 +Total 167 1861.57 2058582553 1019 1009 |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/input/frequency.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/test-data/input/frequency.txt Fri Mar 18 05:22:30 2016 -0400 |
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| b'@@ -0,0 +1,1020 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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/input/frequency_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/test-data/input/frequency_summary.txt Fri Mar 18 05:22:30 2016 -0400 |
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| @@ -0,0 +1,11 @@ +Total number of eQTLs (all) 20206 +Total number of cis-eQTLs 4480 +Total number of trans-eQTLs 12539 +Total number of genes 31036 +Total number of cM 1861.57 +Expected number of eQTL per cM (all) 10.85 +Expected number of cis-eQTL per cM 2.41 +Expected number of trans-eQTL per cM 6.74 +Expected number of genes per cM 16.67 +User specified number of permutations 10 +Number of intervals per sliding window 2 |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/output/._.DS_Store |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/output/._polygon_plot.pdf |
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| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/output/._sliding_frequency.txt |
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|
| b |
| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/test-data/output/sliding_lookup.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/test-data/output/sliding_lookup.txt Fri Mar 18 05:22:30 2016 -0400 |
| [ |
| b'@@ -0,0 +1,843 @@\n+1\t[1, 2]\n+2\t[2, 3]\n+3\t[3, 4, 5]\n+4\t[5, 6]\n+5\t[6, 7]\n+6\t[7, 8]\n+7\t[8, 9]\n+8\t[9, 10, 11]\n+9\t[11, 12]\n+10\t[12, 13]\n+11\t[13, 14]\n+12\t[14, 15]\n+13\t[15, 16]\n+14\t[16, 17]\n+15\t[17, 18]\n+16\t[18, 19]\n+17\t[19, 20, 21]\n+18\t[21, 22]\n+19\t[22, 23, 24]\n+20\t[24, 25]\n+21\t[25, 26, 27]\n+22\t[27, 28]\n+23\t[28, 29, 30]\n+24\t[30, 31]\n+25\t[31, 32]\n+26\t[32, 33]\n+27\t[33, 34]\n+28\t[34, 35]\n+29\t[35, 36]\n+30\t[36, 37]\n+31\t[37, 38, 39]\n+32\t[39, 40]\n+33\t[40, 41]\n+34\t[41, 42]\n+35\t[42, 43]\n+36\t[43, 44, 45]\n+37\t[45, 46]\n+38\t[46, 47]\n+39\t[47, 48]\n+40\t[48, 49]\n+41\t[49, 50]\n+42\t[50, 51]\n+43\t[51, 52, 53]\n+44\t[53, 54]\n+45\t[54, 55]\n+46\t[55, 56]\n+47\t[56, 57]\n+48\t[57, 58]\n+49\t[58, 59]\n+50\t[59, 60]\n+51\t[60, 61, 62]\n+52\t[62, 63]\n+53\t[63, 64]\n+54\t[64, 65]\n+55\t[65, 66]\n+56\t[66, 67]\n+57\t[67, 68]\n+58\t[68, 69, 70]\n+59\t[70, 71]\n+60\t[71, 72]\n+61\t[72, 73]\n+62\t[73, 74]\n+63\t[74, 75]\n+64\t[75, 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1015]\n+842\t[1015, 1016]\n+843\t[1016, 1017, 1018]\n' |
| b |
| diff -r 000000000000 -r 9b835eab8a1d frequency_sliding/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/tool_dependencies.xml Fri Mar 18 05:22:30 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency> + |