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Fix RScript input

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This commit is contained in:
Bryan Roessler
2024-08-04 23:01:10 -04:00
parent 0715c2b150
commit 4059cc965f
7 changed files with 21 additions and 23 deletions
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8
workflow/apps/r/gtaTemplate.R
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@@ -16,25 +16,25 @@ args <- commandArgs(TRUE)
exp_name <- args[1]
if (length(args) > 2) {
if (length(args) >= 2) {
zscores_file <- args[2]
} else {
zscores_file <- "zscores/zscores_interaction.csv" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
}
if (length(args) > 3) {
if (length(args) >= 3) {
sgd_terms_file <- args[3]
} else {
sgd_terms_file <- "go_terms.tab"
}
if (length(args) > 4) {
if (length(args) >= 4) {
sgd_features_file <- args[4]
} else {
sgd_features_file <- "gene_association.sgd" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
}
if (length(args) > 5) {
if (length(args) >= 5) {
output_dir <- args[5]
} else {
output_dir <- "../../out/gta" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd