Mercurial > repos > bgruening > music_construct_eset

annotate scripts/inspect.R @ 1:271f56c5d629 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
author bgruening
date Fri, 26 Nov 2021 15:53:38 +0000
parents 67c243187c1e
children
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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2 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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3 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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5 args <- commandArgs(trailingOnly = TRUE)
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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6 source(args[1])
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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8 printout <- function(text) {
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271f56c5d629 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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9 if (typeof(text) %in% c("list", "vector", "integer", "double", "numeric")) {
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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10 write.table(text, file = outfile_tab, quote = F, sep = "\t",
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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11 col.names = NA)
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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12 } else {
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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13 ## text
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271f56c5d629 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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14 print(typeof(text))
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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15 capture.output(text, file = outfile_tab) # nolint
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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16 }
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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17 }
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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271f56c5d629 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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19 if (inspector %in% c("print", "pData", "fData", "dims",
271f56c5d629 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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20 "experimentData", "protocolData", "exprs",
271f56c5d629 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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21 "signature", "annotation", "abstract")) {
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67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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22 op <- get(inspector)
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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23 tab <- op(rds_eset)
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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24 printout(tab)
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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25 } else {
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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26 stop(paste0("No such option:", inspector))
67c243187c1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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27 }