Mercurial > repos > ethevenot > profia
comparison profia_wrapper.R @ 1:4753e64cf694 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author | ethevenot |
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date | Wed, 03 May 2017 10:49:08 -0400 |
parents | 39ccace77270 |
children | 3f8ae071bdda |
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0:39ccace77270 | 1:4753e64cf694 |
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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") |