Mercurial > repos > ethevenot > profia

comparison profia_wrapper.R @ 1:4753e64cf694 draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author ethevenot
date Wed, 03 May 2017 10:49:08 -0400
parents 39ccace77270
children 3f8ae071bdda
comparison
equal deleted inserted replaced
0:39ccace77270 1:4753e64cf694
95 95
96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") 96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
97 97
98 fiaset <- proFIAset(directory, 98 fiaset <- proFIAset(directory,
99 ppm = as.numeric(argVc["ppmN"]), 99 ppm = as.numeric(argVc["ppmN"]),
100 parallel = FALSE) 100 parallel = TRUE)
101 101
102 stpI <- stpI + 1 102 stpI <- stpI + 1
103 103
104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "") 104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
105 105
180 file = argVc["dataMatrix_out"], 180 file = argVc["dataMatrix_out"],
181 quote = FALSE, 181 quote = FALSE,
182 row.names = FALSE, 182 row.names = FALSE,
183 sep = "\t") 183 sep = "\t")
184 184
185 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), 185 samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
186 samDF) 186 class = samDF[, "class"])
187 write.table(samDF, 187 write.table(samDF,
188 file = argVc["sampleMetadata_out"], 188 file = argVc["sampleMetadata_out"],
189 quote = FALSE, 189 quote = FALSE,
190 row.names = FALSE, 190 row.names = FALSE,
191 sep = "\t") 191 sep = "\t")