Mercurial > repos > recetox > ramclustr

comparison ramclustr_wrapper.R @ 10:2d94da58904b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit dc508ea3521991cd42ff6c1aa8aa845b36412771
author recetox
date Wed, 22 May 2024 08:04:21 +0000
parents c043e1fd79d1
children da7722f665f4
comparison
equal deleted inserted replaced
9:d70dd1d6ac4d 10:2d94da58904b
44 ms1_featurevalues = NULL, 44 ms1_featurevalues = NULL,
45 df_phenodata = NULL, 45 df_phenodata = NULL,
46 phenodata_ext = NULL, 46 phenodata_ext = NULL,
47 exp_des = NULL, 47 exp_des = NULL,
48 st = NULL, 48 st = NULL,
49 ensure_no_na = TRUE) { 49 ensure_no_na = TRUE,
50 ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions) 50 ms1_featuredefinitions_ext = "parquet",
51 ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues) 51 ms1_featurevalues_ext = "parquet") {
52 if (ms1_featuredefinitions_ext == "parquet") {
53 ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
54 } else {
55 ms1_featuredefinitions <- read.csv(ms1_featuredefinitions,
56 header = TRUE, sep = "\t"
57 )
58 }
59
60 if (ms1_featurevalues_ext == "parquet") {
61 ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
62 } else {
63 ms1_featurevalues <- read.csv(ms1_featurevalues, header = TRUE, sep = "\t")
64 }
52 65
53 if (!is.null(df_phenodata)) { 66 if (!is.null(df_phenodata)) {
54 if (phenodata_ext == "csv") { 67 if (phenodata_ext == "csv") {
55 df_phenodata <- read.csv( 68 df_phenodata <- read.csv(
56 file = df_phenodata, 69 file = df_phenodata,