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Updating tools/waveica from version 0.2.0 to 0.2.1 #770

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Merged
mbodova merged 5 commits into from
Jul 13, 2026
Merged

Updating tools/waveica from version 0.2.0 to 0.2.1 #770

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bf4bbfb
Updating tools/waveica from version 0.2.0 to 0.2.1
Jun 16, 2026
2692d43
Merge branch 'master' into tools/waveica
hechth Jun 24, 2026
89f13e8
Merge branch 'master' into tools/waveica
hechth Jul 9, 2026
0dd2973
updated function arguments
mbodova Jul 13, 2026
f69130d
updated test data
mbodova Jul 13, 2026
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2 changes: 1 addition & 1 deletion tools/waveica/macros.xml
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Original file line number Diff line number Diff line change
@@ -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>
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24 changes: 12 additions & 12 deletions tools/waveica/waveica.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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('${__tool_directory__}/waveica_wrapper.R');
Expand All @@ -23,8 +23,8 @@
wavelet_filter = '$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
Expand Down Expand Up @@ -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"/>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
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10 changes: 5 additions & 5 deletions tools/waveica/waveica_wrapper.R
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Expand Up @@ -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) {
Expand All @@ -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
Expand Down Expand Up @@ -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)
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