From bf4bbfbe888e01d91f75f4a29818c17be48eddfe Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Tue, 16 Jun 2026 16:50:54 +0000
Subject: [PATCH 1/3] Updating tools/waveica from version 0.2.0 to 0.2.1

---
 tools/waveica/macros.xml  | 2 +-
 tools/waveica/waveica.xml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/waveica/macros.xml b/tools/waveica/macros.xml
index 04ba14a83..f42130652 100644
--- a/tools/waveica/macros.xml
+++ b/tools/waveica/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.0</token>
+    <token name="@TOOL_VERSION@">0.2.1</token>
 
     <xml name="creator">
         <creator>
diff --git a/tools/waveica/waveica.xml b/tools/waveica/waveica.xml
index faa662cd2..7c39766e9 100644
--- a/tools/waveica/waveica.xml
+++ b/tools/waveica/waveica.xml
@@ -8,8 +8,8 @@
 
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
-        <requirement type="package" version="8.0.0">r-arrow</requirement>
-        <requirement type="package" version="1.0.10">r-dplyr</requirement>
+        <requirement type="package" version="24.0.0">r-arrow</requirement>
+        <requirement type="package" version="1.2.1">r-dplyr</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         Rscript -e "source('${__tool_directory__}/waveica_wrapper.R');

From 0dd297354174ab268ca3590bfa96c1d1dc438d3d Mon Sep 17 00:00:00 2001
From: Michaela Bodova <505814@muni.cz>
Date: Mon, 13 Jul 2026 12:51:09 +0200
Subject: [PATCH 2/3] updated function arguments

---
 tools/waveica/waveica.xml       | 20 ++++++++++----------
 tools/waveica/waveica_wrapper.R | 10 +++++-----
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/tools/waveica/waveica.xml b/tools/waveica/waveica.xml
index 7c39766e9..b160ff308 100644
--- a/tools/waveica/waveica.xml
+++ b/tools/waveica/waveica.xml
@@ -23,8 +23,8 @@
                 wavelet_filter = '$wf.wavelet_filter',
                 wavelet_length = '$wf.wavelet_length',
                 k = $k,
-                t = $batch_correction.t,
-                t2 = $batch_correction.t2,
+                batch_threshold = $batch_correction.batch_threshold,
+                group_threshold = $batch_correction.group_threshold,
                 alpha = $alpha,
                 exclude_blanks = $exclude_blanks,
                 transpose = $transpose_feature_table
@@ -63,8 +63,8 @@
                 <option value="single_batch">Single batch (or no batch information)</option>
             </param>
             <when value="batchwise">
-                <param type="float" value="0.05" name="t" label="Batch-association threshold" help="threshold to consider a component associate with the batch, should be between 0 and 1"/>
-                <param type="float" value="0.05" name="t2" label="Group-association threshold" help="threshold to consider a component associate with the group, should be between 0 and 1"/>
+                <param type="float" value="0.05" name="batch_threshold" label="Batch-association threshold" help="threshold to consider a component associate with the batch, should be between 0 and 1"/>
+                <param type="float" value="0.05" name="group_threshold" label="Group-association threshold" help="threshold to consider a component associate with the group, should be between 0 and 1"/>
             </when>
             <when value="single_batch">
                 <param type="float" value="0" name="cutoff" label="Cutoff" help="threshold of the variation explained by the injection order for independent components, should be between 0 and 1"/>
@@ -87,8 +87,8 @@
             </conditional>
             <conditional name="batch_correction">
                 <param name="mode" value="batchwise"/>
-                <param name="t" value="0.05"/>
-                <param name="t2" value="0.05"/>
+                <param name="batch_threshold" value="0.05"/>
+                <param name="group_threshold" value="0.05"/>
             </conditional>
             <output name="normalized_data" file="test1_output.csv" ftype="csv"/>
         </test>
@@ -103,8 +103,8 @@
             </conditional>
             <conditional name="batch_correction">
                 <param name="mode" value="batchwise"/>
-                <param name="t" value="0.05"/>
-                <param name="t2" value="0.05"/>
+                <param name="batch_threshold" value="0.05"/>
+                <param name="group_threshold" value="0.05"/>
             </conditional>
             <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
         </test>
@@ -119,8 +119,8 @@
             </conditional>
             <conditional name="batch_correction">
                 <param name="mode" value="batchwise"/>
-                <param name="t" value="0.05"/>
-                <param name="t2" value="0.05"/>
+                <param name="batch_threshold" value="0.05"/>
+                <param name="group_threshold" value="0.05"/>
             </conditional>
             <output name="normalized_data" file="test3_output.parquet" compare="sim_size" delta="200" ftype="parquet"/>
         </test>
diff --git a/tools/waveica/waveica_wrapper.R b/tools/waveica/waveica_wrapper.R
index 7f0bc955b..5261eac1d 100644
--- a/tools/waveica/waveica_wrapper.R
+++ b/tools/waveica/waveica_wrapper.R
@@ -53,8 +53,8 @@ waveica <- function(data_matrix_file,
                     wavelet_filter,
                     wavelet_length,
                     k,
-                    t,
-                    t2,
+                    batch_threshold,
+                    group_threshold,
                     alpha,
                     exclude_blanks,
                     transpose = FALSE) {
@@ -75,7 +75,7 @@ waveica <- function(data_matrix_file,
         "injectionOrder", "batch"
     )
 
-    metadata <- dplyr::select(metadata, required_columns)
+    metadata <- dplyr::select(metadata, all_of(required_columns))
 
     # Ensure both tables have a sampleName column
     if (!"sampleName" %in% colnames(features) || !"sampleName" %in% colnames(metadata)) { # nolint
@@ -113,8 +113,8 @@ waveica <- function(data_matrix_file,
         batch = batch,
         group = group,
         K = k,
-        t = t,
-        t2 = t2,
+        batch_threshold = batch_threshold,
+        group_threshold = group_threshold,
         alpha = alpha
     )
     non_feature_columns <- setdiff(colnames(data), feature_columns)

From f69130dcc8c2ebc597720d291ee31b25353ee7fb Mon Sep 17 00:00:00 2001
From: Michaela Bodova <505814@muni.cz>
Date: Mon, 13 Jul 2026 12:51:22 +0200
Subject: [PATCH 3/3] updated test data

---
 .../waveica/test-data/normalized_data.parquet | Bin 3554 -> 2907 bytes
 tools/waveica/test-data/test3_output.parquet  | Bin 3004 -> 2447 bytes
 tools/waveica/test-data/test9_output1.parquet | Bin 3554 -> 2907 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/tools/waveica/test-data/normalized_data.parquet b/tools/waveica/test-data/normalized_data.parquet
index 45cff33e324aa612a57dac93d5eeb69ec6be279c..465aff4680bbfa7fcb9c9fa4ab1e0d5fcde66b09 100644
GIT binary patch
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