Mercurial > repos > iuc > pathview
annotate pathview.r @ 2:fe154a7af404 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
author | iuc |
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date | Fri, 08 Apr 2022 15:36:51 +0000 |
parents | bd99e8fbde97 |
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rev | line source |
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2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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1 error_foo <- function() { |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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2 cat(geterrmessage(), file = stderr()); |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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3 q("no", 1, F) |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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4 } |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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5 options(show.error.messages = F, error = error_foo) |
0
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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6 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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9 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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10 suppressPackageStartupMessages({ |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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11 library("pathview") |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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12 library("optparse") |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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13 }) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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14 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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15 sessionInfo() |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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16 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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17 option_list <- list( |
2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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18 make_option(c("--pathway_id"), type = "character", default = NULL, help = "Path to tabular file with gene data"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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19 make_option(c("--pathway_id_fp"), type = "character", default = NULL, help = "Path to tabular file with pathway ids"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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20 make_option(c("--pathway_id_header"), type = "logical", default = FALSE, help = "Header for tabular file with pathway ids"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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21 make_option(c("--species"), type = "character", default = "hsa", help = "KEGG code, scientific name or the common name of the species"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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22 make_option(c("--gene_data"), type = "character", default = NULL, help = "Path to tabular file with gene data"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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23 make_option(c("--gd_header"), type = "logical", default = FALSE, help = "Header for the gene data file"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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24 make_option(c("--gene_idtype"), type = "character", default = "entrez", help = "ID type used for the gene data"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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25 make_option(c("--cpd_data"), type = "character", default = NULL, help = "Path to tabular file with compound data"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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26 make_option(c("--cpd_header"), type = "logical", default = FALSE, help = "Header for the compound data file"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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27 make_option(c("--cpd_idtype"), type = "character", default = "kegg", help = "ID type used for the compound data"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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28 make_option(c("--multi_state"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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29 make_option(c("--match_data"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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30 make_option(c("--kegg_native"), type = "logical", default = TRUE, help = "Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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31 make_option(c("--same_layer"), type = "logical", default = TRUE, help = "Plot on same layer?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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32 make_option(c("--map_null"), type = "logical", default = TRUE, help = "Map the NULL gene or compound data to pathway?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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33 make_option(c("--split_group"), type = "logical", default = FALSE, help = "Split node groups into individual nodes?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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34 make_option(c("--expand_node"), type = "logical", default = FALSE, help = "Expand multiple-gene nodes into single-gene nodes?"), |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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35 make_option(c("--sign_pos"), type = "character", default = "bottomright", help = "Position of pathview signature") |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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36 ) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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37 |
2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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38 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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39 args <- parse_args(parser) |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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40 print(args) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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41 |
2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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42 read_table <- function(fp, header, rownames = 1, colclasses = NA) { |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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43 table <- read.table(fp, header = header, sep = "\t", row.names = rownames, colClasses = colclasses) |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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44 # transform to vector if only one column |
2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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45 if (dim(table)[2] == 1) { |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
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46 names <- rownames(table) |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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47 table <- table[, 1] |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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48 names(table) <- names |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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49 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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50 return(table) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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51 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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52 |
2
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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53 get_table <- function(fp, header) { |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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54 table <- NULL |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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55 if (!is.null(fp)) { |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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56 table <- read_table(fp, header, rownames = 1) |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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57 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
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58 return(table) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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59 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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60 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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61 # load gene_data file |
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fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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62 gene_data <- get_table(args$gene_data, args$gd_header) |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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63 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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64 # load compound data file |
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fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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65 cpd_data <- get_table(args$cpd_data, args$cpd_header) |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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66 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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67 run_pathview <- function(pathway_id) { |
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bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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68 pathview( |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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69 pathway.id = pathway_id, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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70 gene.data = gene_data, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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71 gene.idtype = args$gene_idtype, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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72 cpd.data = cpd_data, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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73 cpd.idtype = args$cpd_idtype, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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74 species = args$species, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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75 multi.state = args$multi_state, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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76 match.data = args$match_data, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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77 kegg.native = args$kegg_native, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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78 same.layer = args$same_layer, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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79 split.group = args$split_group, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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80 expand.node = args$expand_node, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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81 sign.pos = args$sign_pos, |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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82 map.null = args$map_null) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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83 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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84 |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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85 # get pathway ids |
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fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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86 if (!is.null(args$pathway_id)) { |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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87 run_pathview(args$pathway_id) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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88 } else { |
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89 pthws <- read_table(args$pathway_id_fp, args$pathway_id_header, rownames = NULL, colclasses = "character") |
fe154a7af404
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
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90 for (p in pthws) { |
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91 run_pathview(p) |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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92 } |
bd99e8fbde97
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
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93 } |