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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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1:34f9e847dd4e 2:e1bb35f6ca28
1 }
2 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
3 return(paste0(sample, "-", channel))
4 }
5 coreSampleNames = list()
6 for(i in seq(2, length(multiplexData), 4))
7 {
8 firstGroupNum = 0.75 * i
9 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
10 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
11 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
12 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
13 print(sampleNames[i-1])
14 print(sampleNames[i])
15 print(sampleNames[i+1])
16 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
17 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
18 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
19 }
20 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
21 {
22 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
23 if(is.null(coreSampleNames[[sample]]))
24 {
25 coreSampleNames[[sample]] = 1
26 }
27 else
28 {
29 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
30 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
31 }
32 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
33 coreSampleNames <<- coreSampleNames
34 return(paste0(sample, "-", channel))
35 }
36 coreSampleNames = list()
37 for(i in seq(2, length(multiplexData), 4))
38 {
39 firstGroupNum = 0.75 * i
40 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
41 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
42 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
43 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
44 #print(sampleNames[i-1])
45 #print(sampleNames[i])
46 #print(sampleNames[i+1])
47 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
48 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
49 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
50 }
51 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
52 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
53 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
54 {
55 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
56 if(is.null(coreSampleNames[[sample]]))
57 {
58 coreSampleNames[[sample]] = 1
59 }
60 else
61 {
62 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
63 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
64 }
65 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
66 coreSampleNames <<- coreSampleNames
67 return(paste0(sample, "-", channel))
68 }
69 coreSampleNames = list()
70 for(i in seq(2, length(multiplexData), 4))
71 {
72 firstGroupNum = 0.75 * i
73 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
74 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
75 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
76 print(sampleNames[i-1])
77 print(sampleNames[i])
78 print(sampleNames[i+1])
79 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
80 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
81 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
82 }
83 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
84 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
85 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
86 {
87 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
88 if(is.null(coreSampleNames[[sample]]))
89 {
90 coreSampleNames[[sample]] = 1
91 }
92 else
93 {
94 sample = paste0(sample, "-", incrementChar("A", coreSampleNames[[sample]]))
95 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
96 }
97 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
98 coreSampleNames <<- coreSampleNames
99 return(paste0(sample, "-", channel))
100 }
101 coreSampleNames = list()
102 for(i in seq(2, length(multiplexData), 4))
103 {
104 firstGroupNum = 0.75 * i
105 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
106 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
107 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
108 print(sampleNames[i-1])
109 print(sampleNames[i])
110 print(sampleNames[i+1])
111 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
112 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
113 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
114 }
115 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
116 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
117 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
118 {
119 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
120 if(is.null(coreSampleNames[[sample]]))
121 {
122 coreSampleNames[[sample]] = 1
123 }
124 else
125 {
126 oldCount = coreSampleNames[[sample]]
127 sample = paste0(sample, "-", incrementChar("A", oldCount))
128 coreSampleNames[[sample]] = oldCount + 1
129 }
130 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
131 coreSampleNames <<- coreSampleNames
132 return(paste0(sample, "-", channel))
133 }
134 coreSampleNames = list()
135 for(i in seq(2, length(multiplexData), 4))
136 {
137 firstGroupNum = 0.75 * i
138 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
139 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
140 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
141 print(sampleNames[i-1])
142 print(sampleNames[i])
143 print(sampleNames[i+1])
144 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
145 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
146 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
147 }
148 sort(coreSampleNames)
149 sort(coreSampleNames[1])
150 coreSampleNames[1]
151 coreSampleNames[2]
152 coreSampleNames[1,]
153 coreSampleNames[,1]
154 simplify2array(coreSampleNames)
155 order(coreSampleNames)
156 order(coreSampleNames[1])
157 sort(simplify2array(coreSampleNames))
158 order(coreSampleNames)
159 as.matrix(cores)
160 as.matrix(coreSampleNames)
161 order(as.matrix(coreSampleNames))
162 names(as.matrix(coreSampleNames))
163 names(coreSampleNames)
164 sort(names(coreSampleNames))
165 sort(sampleNames)
166 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
167 sort(sampleNames)
168 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
169 View(ratios)
170 for(i in seq(2, length(multiplexData), 4))
171 {
172 firstGroupNum = 0.75 * i
173 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
174 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
175 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
176 }
177 View(ratios)
178 filepath = "H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct"
179 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
180 source('~/.active-rstudio-document')
181 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
182 demultiplexNetGestaltITRAQ_CCT = function(filepath)
183 {
184 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
185 multiplexData = read.table(filepath, sep="\t", header=T)
186 numSamples = 0.75*(dim(multiplexData)[2]-1)
187 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
188 coreSampleNames = list()
189 for(i in seq(2, length(multiplexData), 4))
190 {
191 firstGroupNum = 0.75 * i
192 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
193 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
194 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
195 }
196 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
197 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
198 for(i in seq(2, length(multiplexData), 4))
199 {
200 firstGroupNum = 0.75 * i
201 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
202 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
203 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
204 }
205 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
206 }
207 source('~/.active-rstudio-document')
208 source('~/.active-rstudio-document')
209 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, sep="\t")
210 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, col.names=T, sep="\t")
211 write.table(format(cbind(rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
212 write.table(format(cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
213 c("GeneSymbol", rownames(ratios))
214 head(c("GeneSymbol", rownames(ratios)))
215 cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4)
216 cbind(c("GeneSymbol", rownames(ratios))
217 )
218 cbind(c("GeneSymbol", rownames(ratios)), ratios)
219 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
220 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
221 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
222 source('~/.active-rstudio-document')
223 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=2))
224 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=4))
225 options(digits=4)
226 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
227 source('~/.active-rstudio-document')
228 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
229 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
230 rm("*")
231 rm("")
232 rm
233 rm()
234 ?rm
235 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
236 {
237 innerSampleNames = coreSampleNames
238 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
239 if(is.null(innerSampleNames[[sample]]))
240 {
241 innerSampleNames[[sample]] = 1
242 }
243 else
244 {
245 oldCount = innerSampleNames[[sample]]
246 sample = paste0(sample, "-", incrementChar("A", oldCount))
247 innerSampleNames[[sample]] = oldCount + 1
248 }
249 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
250 eval.parent(substitute(coreSampleNames = innerSampleNames))
251 return(paste0(sample, "-", channel))
252 }
253 demultiplexNetGestaltITRAQ_CCT = function(filepath)
254 {
255 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
256 multiplexData = read.table(filepath, sep="\t", header=T)
257 numSamples = 0.75*(dim(multiplexData)[2]-1)
258 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
259 coreSampleNames = list()
260 for(i in seq(2, length(multiplexData), 4))
261 {
262 firstGroupNum = 0.75 * i
263 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
264 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
265 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
266 }
267 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
268 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
269 for(i in seq(2, length(multiplexData), 4))
270 {
271 firstGroupNum = 0.75 * i
272 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
273 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
274 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
275 }
276 options(digits=4)
277 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
278 }
279 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
280 ?substittue
281 ?substitute
282 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
283 {
284 innerSampleNames = coreSampleNames
285 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
286 if(is.null(innerSampleNames[[sample]]))
287 {
288 innerSampleNames[[sample]] = 1
289 }
290 else
291 {
292 oldCount = innerSampleNames[[sample]]
293 sample = paste0(sample, "-", incrementChar("A", oldCount))
294 innerSampleNames[[sample]] = oldCount + 1
295 }
296 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
297 eval.parent(substitute(coreSampleNames<-innerSampleNames))
298 return(paste0(sample, "-", channel))
299 }
300 demultiplexNetGestaltITRAQ_CCT = function(filepath)
301 {
302 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
303 multiplexData = read.table(filepath, sep="\t", header=T)
304 numSamples = 0.75*(dim(multiplexData)[2]-1)
305 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
306 coreSampleNames = list()
307 for(i in seq(2, length(multiplexData), 4))
308 {
309 firstGroupNum = 0.75 * i
310 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
311 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
312 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
313 }
314 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
315 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
316 for(i in seq(2, length(multiplexData), 4))
317 {
318 firstGroupNum = 0.75 * i
319 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
320 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
321 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
322 }
323 options(digits=4)
324 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
325 }
326 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
327 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct")
328 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
329 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
330 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
331 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
332 ratios_ordered = ratios[,order(names(ratios))]
333 ratios_ordered = ratios[order(names(ratios)),]
334 names(ratios)
335 colnames(ratios)
336 ratios_ordered = ratios[order(colnames(ratios)),]
337 ratios_ordered = ratios[,order(colnames(ratios))]
338 View(ratios_ordered)
339 source('~/.active-rstudio-document')
340 source('~/.active-rstudio-document')
341 source('~/.active-rstudio-document')
342 source('~/.active-rstudio-document')
343 biocLite("RGalaxy")
344 source("https://bioconductor.org/biocLite.R")
345 biocLite("RGalaxy")
346 source('~/.active-rstudio-document')
347 source('~/.active-rstudio-document')
348 source('~/.active-rstudio-document')
349 galaxyHome="/galaxy-central"
350 galaxy("addTwoNumbers",
351 galaxyConfig=
352 GalaxyConfig(galaxyHome, "mytool", "Test Section",
353 "testSectionId")
354 )
355 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
356 galaxy("addTwoNumbers",
357 galaxyConfig=
358 GalaxyConfig(galaxyHome, "mytool", "Test Section",
359 "testSectionId")
360 )
361 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
362 galaxy("addTwoNumbers",
363 galaxyConfig=
364 GalaxyConfig(galaxyHome, "mytool", "Test Section",
365 "testSectionId")
366 )
367 ?GalaxyConfig
368 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
369 galaxy("addTwoNumbers",
370 galaxyConfig=
371 GalaxyConfig(galaxyHome, "mytool", "Test Section",
372 "testSectionId")
373 )
374 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
375 galaxy("addTwoNumbers",
376 galaxyConfig=
377 GalaxyConfig(galaxyHome, "mytool", "Test Section",
378 "testSectionId")
379 )
380 source('~/.active-rstudio-document')
381 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
382 galaxy("addTwoNumbers",
383 galaxyConfig=
384 GalaxyConfig(galaxyHome, "mytool", "Test Section",
385 "testSectionId")
386 )
387 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
388 galaxy("addTwoNumbers",
389 galaxyConfig=
390 GalaxyConfig(galaxyHome, "mytool", "Test Section",
391 "testSectionId")
392 )
393 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
394 galaxy("PrepareAnnotationGENCODE_g",
395 galaxyConfig=
396 GalaxyConfig(galaxyHome, "mytool", "Test Section",
397 "testSectionId")
398 )
399 PrepareAnnotationGENCODE_g <- function() {}
400 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
401 galaxy("PrepareAnnotationGENCODE_g",
402 galaxyConfig=
403 GalaxyConfig(galaxyHome, "mytool", "Test Section",
404 "testSectionId")
405 )
406 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
407 CDSfasta = GalaxyInputFile(required = TRUE),
408 pepfasta = GalaxyInputFile(required = TRUE),
409 annotation_path = GalaxyCharacterParam(required = TRUE),
410 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
411 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
412 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
413 {
414 }
415 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
416 CDSfasta = GalaxyInputFile(required = TRUE),
417 pepfasta = GalaxyInputFile(required = TRUE),
418 annotation_path = GalaxyCharacterParam(required = TRUE),
419 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
420 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
421 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
422 {
423 }
424 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
425 galaxy("PrepareAnnotationGENCODE_g",
426 galaxyConfig=
427 GalaxyConfig(galaxyHome, "mytool", "Test Section",
428 "testSectionId")
429 )
430 source('~/.active-rstudio-document')
431 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
432 CDSfasta = GalaxyInputFile(required = TRUE),
433 pepfasta = GalaxyInputFile(required = TRUE),
434 annotation_path = GalaxyCharacterParam(required = TRUE),
435 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
436 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
437 COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
438 {
439 }
440 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
441 galaxy("PrepareAnnotationGENCODE_g",
442 galaxyConfig=
443 GalaxyConfig(galaxyHome, "mytool", "Test Section",
444 "testSectionId")
445 )
446 source('~/.active-rstudio-document')
447 source('~/.active-rstudio-document')
448 source('~/.active-rstudio-document')
449 source('~/.active-rstudio-document')
450 source('~/.active-rstudio-document')
451 source('~/.active-rstudio-document')
452 source('~/.active-rstudio-document')
453 source('~/.active-rstudio-document')
454 ?wtf
455 print "why doesn't this work"
456 print( )"why doesn't this work")
457 print("why doesn't this work")
458 source('~/.active-rstudio-document')
459 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
460 galaxy("addTwoNumbers",
461 galaxyConfig=
462 GalaxyConfig(galaxyHome, "mytool", "Test Section",
463 "testSectionId")
464 )
465 source('~/.active-rstudio-document')
466 source('~/.active-rstudio-document')
467 PrepareAnnotationGENCODE <- function(gtfFile = GalaxyInputFile(required = TRUE),
468 CDSfasta = GalaxyInputFile(required = TRUE),
469 pepfasta = GalaxyInputFile(required = TRUE),
470 annotation_path = GalaxyCharacterParam(required = TRUE),
471 COSMIC = GalaxyLogicalParam(checked = TRUE),
472 output = GalaxyOutput("sum", "txt"))
473 {
474 print("why doesn't this work")
475 }
476 source('~/.active-rstudio-document')
477 source('~/.active-rstudio-document')
478 source('~/.active-rstudio-document')
479 library(RGalaxy)
480 source('~/.active-rstudio-document')
481 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
482 galaxy("PrepareAnnotationGENCODE",
483 galaxyConfig=
484 GalaxyConfig(galaxyHome, "mytool", "Test Section",
485 "testSectionId")
486 )
487 source('~/.active-rstudio-document')
488 str(addTwoNumbers)
489 addTwoNumbers
490 packageName()
491 packageName(addTwoNumbers)
492 packageName("addTwoNumbers")
493 source('~/.active-rstudio-document')
494 source('~/.active-rstudio-document', echo=TRUE)
495 source('~/.active-rstudio-document', echo=TRUE)
496 str(addTwoNumbers)
497 str(addTwoNumbers2)
498 env(addTwoNumbers)
499 environmentName
500 environmentName()
501 env.profile()
502 namespace:base
503 library(namespace)
504 source('~/.active-rstudio-document', echo=TRUE)
505 source("https://bioconductor.org/biocLite.R")
506 biocLite("customProDB")
507 library("customProDB", lib.loc="C:/Users/chambem2/Google Drive/Marvin Documents/R/win-library/3.1")
508 setwd("C:/Users/chambem2/.vagrant/precise64/bingomics-galaxy/vagrant/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data")
509 bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB")
510 easyRun(bamFile=bamFile, annotation_path=".")
511 easyRun(bamFile=bamFile, annotation_path=".")
512 easyRun(bamFile=bamFile, annotation_path=".", outfile_path=".", outfile_name="test.fasta")