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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 14 Jan 2016 18:13:18 -0500
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e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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1 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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2 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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3 return(paste0(sample, "-", channel))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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4 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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5 coreSampleNames = list()
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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6 for(i in seq(2, length(multiplexData), 4))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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7 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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8 firstGroupNum = 0.75 * i
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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9 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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10 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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11 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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12 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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13 print(sampleNames[i-1])
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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14 print(sampleNames[i])
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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15 print(sampleNames[i+1])
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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16 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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17 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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18 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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19 }
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20 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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21 {
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22 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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23 if(is.null(coreSampleNames[[sample]]))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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24 {
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25 coreSampleNames[[sample]] = 1
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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26 }
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27 else
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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28 {
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29 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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30 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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31 }
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32 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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33 coreSampleNames <<- coreSampleNames
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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34 return(paste0(sample, "-", channel))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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35 }
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36 coreSampleNames = list()
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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37 for(i in seq(2, length(multiplexData), 4))
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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38 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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39 firstGroupNum = 0.75 * i
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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40 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
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41 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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42 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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43 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
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44 #print(sampleNames[i-1])
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45 #print(sampleNames[i])
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46 #print(sampleNames[i+1])
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47 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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48 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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49 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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50 }
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51 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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52 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
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53 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
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54 {
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55 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
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56 if(is.null(coreSampleNames[[sample]]))
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57 {
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58 coreSampleNames[[sample]] = 1
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59 }
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60 else
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61 {
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62 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
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63 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
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64 }
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65 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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66 coreSampleNames <<- coreSampleNames
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67 return(paste0(sample, "-", channel))
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68 }
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69 coreSampleNames = list()
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70 for(i in seq(2, length(multiplexData), 4))
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71 {
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72 firstGroupNum = 0.75 * i
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73 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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74 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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75 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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76 print(sampleNames[i-1])
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77 print(sampleNames[i])
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78 print(sampleNames[i+1])
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79 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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80 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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81 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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82 }
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83 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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84 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
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85 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
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86 {
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87 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
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88 if(is.null(coreSampleNames[[sample]]))
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89 {
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90 coreSampleNames[[sample]] = 1
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91 }
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92 else
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93 {
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94 sample = paste0(sample, "-", incrementChar("A", coreSampleNames[[sample]]))
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95 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
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96 }
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97 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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98 coreSampleNames <<- coreSampleNames
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99 return(paste0(sample, "-", channel))
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100 }
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101 coreSampleNames = list()
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102 for(i in seq(2, length(multiplexData), 4))
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103 {
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104 firstGroupNum = 0.75 * i
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105 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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106 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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107 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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108 print(sampleNames[i-1])
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109 print(sampleNames[i])
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110 print(sampleNames[i+1])
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111 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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112 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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113 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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114 }
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115 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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116 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
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117 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
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118 {
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119 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
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120 if(is.null(coreSampleNames[[sample]]))
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121 {
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122 coreSampleNames[[sample]] = 1
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123 }
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124 else
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125 {
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126 oldCount = coreSampleNames[[sample]]
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127 sample = paste0(sample, "-", incrementChar("A", oldCount))
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128 coreSampleNames[[sample]] = oldCount + 1
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129 }
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130 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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131 coreSampleNames <<- coreSampleNames
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132 return(paste0(sample, "-", channel))
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133 }
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134 coreSampleNames = list()
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135 for(i in seq(2, length(multiplexData), 4))
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136 {
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137 firstGroupNum = 0.75 * i
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138 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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139 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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140 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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141 print(sampleNames[i-1])
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142 print(sampleNames[i])
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143 print(sampleNames[i+1])
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144 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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145 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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146 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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147 }
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148 sort(coreSampleNames)
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149 sort(coreSampleNames[1])
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150 coreSampleNames[1]
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151 coreSampleNames[2]
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152 coreSampleNames[1,]
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153 coreSampleNames[,1]
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154 simplify2array(coreSampleNames)
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155 order(coreSampleNames)
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156 order(coreSampleNames[1])
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157 sort(simplify2array(coreSampleNames))
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158 order(coreSampleNames)
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159 as.matrix(cores)
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160 as.matrix(coreSampleNames)
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161 order(as.matrix(coreSampleNames))
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162 names(as.matrix(coreSampleNames))
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163 names(coreSampleNames)
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164 sort(names(coreSampleNames))
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165 sort(sampleNames)
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166 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
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167 sort(sampleNames)
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168 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
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169 View(ratios)
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170 for(i in seq(2, length(multiplexData), 4))
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171 {
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172 firstGroupNum = 0.75 * i
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173 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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174 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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175 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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176 }
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177 View(ratios)
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178 filepath = "H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct"
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179 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
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180 source('~/.active-rstudio-document')
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181 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
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182 demultiplexNetGestaltITRAQ_CCT = function(filepath)
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183 {
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184 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
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185 multiplexData = read.table(filepath, sep="\t", header=T)
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186 numSamples = 0.75*(dim(multiplexData)[2]-1)
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187 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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188 coreSampleNames = list()
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189 for(i in seq(2, length(multiplexData), 4))
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190 {
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191 firstGroupNum = 0.75 * i
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192 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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193 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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194 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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195 }
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196 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
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197 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
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198 for(i in seq(2, length(multiplexData), 4))
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199 {
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200 firstGroupNum = 0.75 * i
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201 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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202 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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203 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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204 }
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205 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
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206 }
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207 source('~/.active-rstudio-document')
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208 source('~/.active-rstudio-document')
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209 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, sep="\t")
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210 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, col.names=T, sep="\t")
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211 write.table(format(cbind(rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
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212 write.table(format(cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
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213 c("GeneSymbol", rownames(ratios))
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214 head(c("GeneSymbol", rownames(ratios)))
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215 cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4)
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216 cbind(c("GeneSymbol", rownames(ratios))
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217 )
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218 cbind(c("GeneSymbol", rownames(ratios)), ratios)
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219 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
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220 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
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221 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
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222 source('~/.active-rstudio-document')
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223 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=2))
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224 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=4))
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225 options(digits=4)
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226 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
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227 source('~/.active-rstudio-document')
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228 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
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229 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
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230 rm("*")
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231 rm("")
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232 rm
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233 rm()
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234 ?rm
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235 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
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236 {
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237 innerSampleNames = coreSampleNames
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238 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
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239 if(is.null(innerSampleNames[[sample]]))
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240 {
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241 innerSampleNames[[sample]] = 1
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242 }
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243 else
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244 {
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245 oldCount = innerSampleNames[[sample]]
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246 sample = paste0(sample, "-", incrementChar("A", oldCount))
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247 innerSampleNames[[sample]] = oldCount + 1
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248 }
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249 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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250 eval.parent(substitute(coreSampleNames = innerSampleNames))
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251 return(paste0(sample, "-", channel))
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252 }
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253 demultiplexNetGestaltITRAQ_CCT = function(filepath)
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254 {
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255 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
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256 multiplexData = read.table(filepath, sep="\t", header=T)
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257 numSamples = 0.75*(dim(multiplexData)[2]-1)
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258 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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259 coreSampleNames = list()
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260 for(i in seq(2, length(multiplexData), 4))
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261 {
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262 firstGroupNum = 0.75 * i
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263 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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264 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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265 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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266 }
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267 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
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268 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
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269 for(i in seq(2, length(multiplexData), 4))
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270 {
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271 firstGroupNum = 0.75 * i
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272 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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273 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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274 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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275 }
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276 options(digits=4)
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277 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
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278 }
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279 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
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280 ?substittue
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diff changeset
281 ?substitute
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282 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
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283 {
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284 innerSampleNames = coreSampleNames
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285 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
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286 if(is.null(innerSampleNames[[sample]]))
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287 {
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288 innerSampleNames[[sample]] = 1
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289 }
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290 else
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291 {
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292 oldCount = innerSampleNames[[sample]]
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293 sample = paste0(sample, "-", incrementChar("A", oldCount))
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294 innerSampleNames[[sample]] = oldCount + 1
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295 }
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296 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
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297 eval.parent(substitute(coreSampleNames<-innerSampleNames))
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298 return(paste0(sample, "-", channel))
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299 }
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300 demultiplexNetGestaltITRAQ_CCT = function(filepath)
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301 {
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302 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
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303 multiplexData = read.table(filepath, sep="\t", header=T)
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304 numSamples = 0.75*(dim(multiplexData)[2]-1)
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305 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
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306 coreSampleNames = list()
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307 for(i in seq(2, length(multiplexData), 4))
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308 {
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309 firstGroupNum = 0.75 * i
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310 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
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diff changeset
311 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
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galaxyp
parents:
diff changeset
312 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
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parents:
diff changeset
313 }
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galaxyp
parents:
diff changeset
314 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
315 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
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galaxyp
parents:
diff changeset
316 for(i in seq(2, length(multiplexData), 4))
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galaxyp
parents:
diff changeset
317 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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parents:
diff changeset
318 firstGroupNum = 0.75 * i
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parents:
diff changeset
319 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
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galaxyp
parents:
diff changeset
320 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
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galaxyp
parents:
diff changeset
321 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
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parents:
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322 }
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galaxyp
parents:
diff changeset
323 options(digits=4)
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324 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
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325 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
326 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
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galaxyp
parents:
diff changeset
327 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct")
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diff changeset
328 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
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diff changeset
329 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
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parents:
diff changeset
330 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
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parents:
diff changeset
331 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
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diff changeset
332 ratios_ordered = ratios[,order(names(ratios))]
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diff changeset
333 ratios_ordered = ratios[order(names(ratios)),]
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334 names(ratios)
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diff changeset
335 colnames(ratios)
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336 ratios_ordered = ratios[order(colnames(ratios)),]
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337 ratios_ordered = ratios[,order(colnames(ratios))]
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338 View(ratios_ordered)
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339 source('~/.active-rstudio-document')
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340 source('~/.active-rstudio-document')
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341 source('~/.active-rstudio-document')
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342 source('~/.active-rstudio-document')
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343 biocLite("RGalaxy")
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344 source("https://bioconductor.org/biocLite.R")
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345 biocLite("RGalaxy")
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346 source('~/.active-rstudio-document')
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347 source('~/.active-rstudio-document')
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348 source('~/.active-rstudio-document')
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349 galaxyHome="/galaxy-central"
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350 galaxy("addTwoNumbers",
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351 galaxyConfig=
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352 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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353 "testSectionId")
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354 )
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355 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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356 galaxy("addTwoNumbers",
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357 galaxyConfig=
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358 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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diff changeset
359 "testSectionId")
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360 )
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361 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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362 galaxy("addTwoNumbers",
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363 galaxyConfig=
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364 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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diff changeset
365 "testSectionId")
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366 )
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367 ?GalaxyConfig
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368 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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369 galaxy("addTwoNumbers",
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370 galaxyConfig=
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371 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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diff changeset
372 "testSectionId")
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373 )
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374 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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375 galaxy("addTwoNumbers",
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376 galaxyConfig=
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377 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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diff changeset
378 "testSectionId")
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379 )
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380 source('~/.active-rstudio-document')
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381 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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382 galaxy("addTwoNumbers",
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383 galaxyConfig=
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384 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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385 "testSectionId")
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386 )
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387 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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388 galaxy("addTwoNumbers",
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389 galaxyConfig=
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parents:
diff changeset
390 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
391 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
392 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
393 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
394 galaxy("PrepareAnnotationGENCODE_g",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
395 galaxyConfig=
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
396 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
397 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
398 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
399 PrepareAnnotationGENCODE_g <- function() {}
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
400 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
401 galaxy("PrepareAnnotationGENCODE_g",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
402 galaxyConfig=
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
403 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
404 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
405 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
406 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
407 CDSfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
408 pepfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
409 annotation_path = GalaxyCharacterParam(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
410 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
411 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
412 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
413 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
414 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
415 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
416 CDSfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
417 pepfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
418 annotation_path = GalaxyCharacterParam(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
419 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
420 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
421 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
422 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
423 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
424 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
425 galaxy("PrepareAnnotationGENCODE_g",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
426 galaxyConfig=
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
427 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
428 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
429 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
430 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
431 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
432 CDSfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
433 pepfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
434 annotation_path = GalaxyCharacterParam(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
435 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
436 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
437 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
438 {
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
439 }
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
440 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
441 galaxy("PrepareAnnotationGENCODE_g",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
442 galaxyConfig=
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
443 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
444 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
445 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
446 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
447 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
448 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
449 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
450 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
451 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
452 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
453 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
454 ?wtf
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
455 print "why doesn't this work"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
456 print( )"why doesn't this work")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
457 print("why doesn't this work")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
458 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
459 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
460 galaxy("addTwoNumbers",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
461 galaxyConfig=
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
462 GalaxyConfig(galaxyHome, "mytool", "Test Section",
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
463 "testSectionId")
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
464 )
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
465 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
466 source('~/.active-rstudio-document')
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
467 PrepareAnnotationGENCODE <- function(gtfFile = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
468 CDSfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
469 pepfasta = GalaxyInputFile(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
470 annotation_path = GalaxyCharacterParam(required = TRUE),
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
471 COSMIC = GalaxyLogicalParam(checked = TRUE),
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472 output = GalaxyOutput("sum", "txt"))
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473 {
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galaxyp
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diff changeset
474 print("why doesn't this work")
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galaxyp
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diff changeset
475 }
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galaxyp
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476 source('~/.active-rstudio-document')
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galaxyp
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diff changeset
477 source('~/.active-rstudio-document')
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galaxyp
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diff changeset
478 source('~/.active-rstudio-document')
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galaxyp
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479 library(RGalaxy)
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galaxyp
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480 source('~/.active-rstudio-document')
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481 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
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482 galaxy("PrepareAnnotationGENCODE",
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diff changeset
483 galaxyConfig=
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484 GalaxyConfig(galaxyHome, "mytool", "Test Section",
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galaxyp
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485 "testSectionId")
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diff changeset
486 )
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galaxyp
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487 source('~/.active-rstudio-document')
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galaxyp
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488 str(addTwoNumbers)
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diff changeset
489 addTwoNumbers
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diff changeset
490 packageName()
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diff changeset
491 packageName(addTwoNumbers)
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diff changeset
492 packageName("addTwoNumbers")
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493 source('~/.active-rstudio-document')
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494 source('~/.active-rstudio-document', echo=TRUE)
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495 source('~/.active-rstudio-document', echo=TRUE)
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diff changeset
496 str(addTwoNumbers)
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497 str(addTwoNumbers2)
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498 env(addTwoNumbers)
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499 environmentName
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500 environmentName()
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501 env.profile()
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502 namespace:base
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503 library(namespace)
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504 source('~/.active-rstudio-document', echo=TRUE)
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505 source("https://bioconductor.org/biocLite.R")
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506 biocLite("customProDB")
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507 library("customProDB", lib.loc="C:/Users/chambem2/Google Drive/Marvin Documents/R/win-library/3.1")
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508 setwd("C:/Users/chambem2/.vagrant/precise64/bingomics-galaxy/vagrant/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data")
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509 bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB")
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diff changeset
510 easyRun(bamFile=bamFile, annotation_path=".")
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511 easyRun(bamFile=bamFile, annotation_path=".")
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512 easyRun(bamFile=bamFile, annotation_path=".", outfile_path=".", outfile_name="test.fasta")