| Previous changeset 8:bf32ae95a06f (2024-08-06) Next changeset 10:821062fc5782 (2025-07-04) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit bbcbf9c32acaedffb78f0caef47faeed8f68cb52 |
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modified:
macros.xml waveica.xml waveica_wrapper.R |
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| 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 |
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| @@ -22,29 +22,14 @@ <xml name="annotation"> <xrefs> - <xref type="bio.tools">waveica</xref> + <xref type="bio.tools">waveica</xref> </xrefs> </xml> <xml name="input_data"> - <param type="data" name="data" label="Feature table" format="csv,tsv,parquet" help=""/> - </xml> - <xml name="general_parameters"> - <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/> - <param type="float" value="0" name="alpha" label="Alpha" help="trade-off value between the independence of samples (temporal ICA) and variables (spatial ICA), should be between 0 and 1"/> + <param type="data" name="data" label="Feature table" format="csv,tsv,tabular,parquet" help=""/> </xml> - <xml name="batchwise_parameters"> - <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"/> - </xml> - <xml name="singlebatch_parameters"> - <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"/> - </xml> - <xml name="exclude_blanks"> - <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" /> - </xml> + <xml name="wf"> <conditional name="wf"> <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="wavelet function and filter length [1] (see footnotes for more details)"> |
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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 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy8" profile="21.09">\n+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy9" profile="23.0">\n <description>removal of batch effects for untargeted metabolomics data</description>\n <macros>\n <import>macros.xml</import>\n@@ -18,8 +18,8 @@\n -e \'normalized_data <- waveica(\n file = "$input_num.data",\n #if $input_num.input_choice == "2":\n- metadata = "$input_num.input_metadata.metadata",\n- ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",\n+ metadata = "$input_num.metadata",\n+ ext = "$input_num.data.ext,$input_num.metadata.ext",\n transpose = $input_num.transpose_feature_table,\n #else:\n ext = "$input_num.data.ext",\n@@ -36,8 +36,8 @@\n -e \'normalized_data <- waveica_singlebatch( \n file = "$input_num.data",\n #if $input_num.input_choice == "2":\n- metadata = "$input_num.input_metadata.metadata",\n- ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",\n+ metadata = "$input_num.metadata",\n+ ext = "$input_num.data.ext,$input_num.metadata.ext",\n transpose = $input_num.transpose_feature_table,\n #else:\n ext = "$input_num.data.ext",\n@@ -65,14 +65,13 @@\n </when>\n <when value="2">\n <expand macro="input_data"/>\n- <section name="input_metadata" title="Input metadata table" expanded="true">\n- <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" />\n- </section>\n+ <param name="metadata" label="Input metadata" type="data" format="csv,tsv,tabular,parquet" help="" />\n <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false" \n truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />\n </when>\n </conditional>\n- <expand macro="general_parameters"/>\n+ <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>\n+ <param type="float" value="0" name="alpha" label="Alpha" help="trade-off value between the independence of samples (temporal ICA) and variables (spatial ICA), should be between 0 and 1"/>\n <expand macro="wf"/>\n <conditional name="batch_correction">\n <param name="mode" type="select" label="Batch correction mode" help="\'multiple batches\' takes into account\n@@ -82,13 +81,14 @@\n <option value="single_batch">Single batch (or no batch information)</option>\n </param>\n <when value="batchwise">\n- <expand macro="batchwise_parameters"/>\n+ <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"/>\n+ <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"/>\n </when>\n <when value="single_batch">\n- <expand macro="singlebatch_parameters"/>\n+ <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"/>\n </when>\n </conditional>\n- <expand macro="exclude_blanks"/>\n+ <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falseva'..b'v"/>\n+ <param name="transpose_feature_table" value="TRUE"/>\n+ </conditional>\n <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>\n </test>\n- <!-- The following test has different results on three platform I\'ve tried -->\n- <!-- <test>\n- <param name="data" value="input_data_nobatch.csv" ftype="csv"/>\n- <param name="mode" value="single_batch"/>\n- <param name="wavelet_filter" value="d"/>\n- <param name="filter_length" value="2"/>\n- <param name="k" value="20"/>\n- <param name="alpha" value="0"/>\n- <param name="cutoff" value="0"/>\n- <output name="normalized_data" file="normalized_data_nobatch.tsv"/>\n- </test> -->\n <test expect_num_outputs="2"><!-- TEST 9 -->\n- <param name="input_choice" value="2"/>\n- <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>\n- <param name="metadata" value="metadata.parquet" ftype="parquet"/>\n- <param name="transpose_feature_table" value="TRUE"/>\n- <param name="mode" value="batchwise"/>\n- <param name="wavelet_filter" value="d"/>\n- <param name="wavelet_length" value="2"/>\n- <param name="k" value="20"/>\n- <param name="t" value="0.05"/>\n- <param name="t2" value="0.05"/>\n- <param name="alpha" value="0"/>\n+ <conditional name="input_num">\n+ <param name="input_choice" value="2"/>\n+ <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>\n+ <param name="metadata" value="metadata.parquet" ftype="parquet"/>\n+ <param name="transpose_feature_table" value="TRUE"/>\n+ </conditional>\n <param name="keep_two_output" value="TRUE"/>\n <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>\n <output name="metadata" file="test9_output2.parquet" ftype="parquet"/>\n </test>\n <test expect_num_outputs="2"><!-- TEST 10 -->\n- <param name="input_choice" value="2"/>\n- <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>\n- <param name="metadata" value="metadata.csv" ftype="csv"/>\n- <param name="transpose_feature_table" value="TRUE"/>\n- <param name="mode" value="batchwise"/>\n- <param name="wavelet_filter" value="d"/>\n- <param name="wavelet_length" value="2"/>\n- <param name="k" value="20"/>\n- <param name="t" value="0.05"/>\n- <param name="t2" value="0.05"/>\n- <param name="alpha" value="0"/>\n+ <conditional name="input_num">\n+ <param name="input_choice" value="2"/>\n+ <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>\n+ <param name="metadata" value="metadata.csv" ftype="csv"/>\n+ <param name="transpose_feature_table" value="TRUE"/>\n+ </conditional>\n <param name="keep_two_output" value="TRUE"/>\n <output name="normalized_data" file="test10_output1.tsv" ftype="tabular"/>\n <output name="metadata" file="test10_output2.tsv" ftype="tabular"/>\n </test>\n <test expect_failure="true"><!-- TEST 11 -->\n- <param name="data" value="na_data.csv" ftype="csv"/>\n+ <conditional name="input_num">\n+ <param name="data" value="na_data.csv" ftype="csv"/>\n+ </conditional>\n </test>\n <test expect_failure="true"><!-- TEST 12 -->\n- <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>\n+ <conditional name="input_num">\n+ <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>\n+ </conditional>\n </test>\n </tests>\n \n' |
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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 |
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| @@ -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) |