Mercurial > repos > recetox > ramclustr

diff 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
line wrap: on
line diff
--- a/ramclustr_wrapper.R	Wed Apr 17 07:51:23 2024 +0000
+++ b/ramclustr_wrapper.R	Wed May 22 08:04:21 2024 +0000
@@ -46,9 +46,22 @@
                                   phenodata_ext = NULL,
                                   exp_des = NULL,
                                   st = NULL,
-                                  ensure_no_na = TRUE) {
-  ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
-  ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
+                                  ensure_no_na = TRUE,
+                                  ms1_featuredefinitions_ext = "parquet",
+                                  ms1_featurevalues_ext = "parquet") {
+  if (ms1_featuredefinitions_ext == "parquet") {
+    ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
+  } else {
+    ms1_featuredefinitions <- read.csv(ms1_featuredefinitions,
+      header = TRUE, sep = "\t"
+    )
+  }
+
+  if (ms1_featurevalues_ext == "parquet") {
+    ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
+  } else {
+    ms1_featurevalues <- read.csv(ms1_featurevalues, header = TRUE, sep = "\t")
+  }
 
   if (!is.null(df_phenodata)) {
     if (phenodata_ext == "csv") {