# HG changeset patch
# User recetox
# Date 1747390467 0
# Node ID 6fc9f6dbcef5da6d83331c89c4fe64dd75aae531
# Parent bf32ae95a06f88e03f623cea03f39ad138571d00
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit bbcbf9c32acaedffb78f0caef47faeed8f68cb52
diff -r bf32ae95a06f -r 6fc9f6dbcef5 macros.xml
--- a/macros.xml Tue Aug 06 14:27:48 2024 +0000
+++ b/macros.xml Fri May 16 10:14:27 2025 +0000
@@ -22,29 +22,14 @@
- waveica
+ waveica
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diff -r bf32ae95a06f -r 6fc9f6dbcef5 waveica.xml
--- a/waveica.xml Tue Aug 06 14:27:48 2024 +0000
+++ b/waveica.xml Fri May 16 10:14:27 2025 +0000
@@ -1,4 +1,4 @@
-
+
removal of batch effects for untargeted metabolomics data
macros.xml
@@ -18,8 +18,8 @@
-e 'normalized_data <- waveica(
file = "$input_num.data",
#if $input_num.input_choice == "2":
- metadata = "$input_num.input_metadata.metadata",
- ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
+ metadata = "$input_num.metadata",
+ ext = "$input_num.data.ext,$input_num.metadata.ext",
transpose = $input_num.transpose_feature_table,
#else:
ext = "$input_num.data.ext",
@@ -36,8 +36,8 @@
-e 'normalized_data <- waveica_singlebatch(
file = "$input_num.data",
#if $input_num.input_choice == "2":
- metadata = "$input_num.input_metadata.metadata",
- ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
+ metadata = "$input_num.metadata",
+ ext = "$input_num.data.ext,$input_num.metadata.ext",
transpose = $input_num.transpose_feature_table,
#else:
ext = "$input_num.data.ext",
@@ -65,14 +65,13 @@
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Single batch (or no batch information)
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@@ -96,153 +96,140 @@
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diff -r bf32ae95a06f -r 6fc9f6dbcef5 waveica_wrapper.R
--- a/waveica_wrapper.R Tue Aug 06 14:27:48 2024 +0000
+++ b/waveica_wrapper.R Fri May 16 10:14:27 2025 +0000
@@ -17,7 +17,7 @@
read_data <- function(file, ext) {
if (ext == "csv") {
data <- read.csv(file, header = TRUE)
- } else if (ext == "tsv") {
+ } else if (ext == "tsv" || ext == "tabular") {
data <- read.csv(file, header = TRUE, sep = "\t")
} else {
data <- arrow::read_parquet(file)