Mercurial > repos > recetox > waveica
view waveica.xml @ 0:328710890963 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
author | recetox |
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date | Wed, 23 Mar 2022 11:35:30 +0000 |
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children | b77023c41c76 |
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<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy1" python_template_version="3.5"> <description>removal of batch effects for untargeted metabolomics data</description> <macros> <import>macros.xml</import> </macros> <expand macro="creator"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ Rscript -e 'source("${__tool_directory__}/waveica_wrapper.R")' #if $batch_correction.mode == "batchwise": -e 'normalized_data <- waveica( data = "$data", wavelet_filter = "$wf.wavelet_filter", wavelet_length = "$wf.wavelet_length", k = $k, t = $batch_correction.t, t2 = $batch_correction.t2, alpha = $alpha, exclude_blanks = $exclude_blanks )' #else if $batch_correction.mode == "single_batch": -e 'normalized_data <- waveica_singlebatch( data = "$data", wavelet_filter = "$wf.wavelet_filter", wavelet_length = "$wf.wavelet_length", k = $k, alpha = $alpha, cutoff = $batch_correction.cutoff, exclude_blanks = $exclude_blanks )' #end if -e 'store_data(normalized_data,"$normalized_data")' ]]></command> <inputs> <expand macro="general_parameters"/> <expand macro="wf"/> <conditional name="batch_correction"> <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and requires no batch information [2]"> <option value="batchwise" selected="true">Multiple batches</option> <option value="single_batch">Single batch (or no batch information)</option> </param> <when value="batchwise"> <expand macro="batchwise_parameters"/> </when> <when value="single_batch"> <expand macro="singlebatch_parameters"/> </when> </conditional> <expand macro="exclude_blanks"/> </inputs> <expand macro="outputs"/> <tests> <test> <param name="data" value="input_data.csv" ftype="csv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> <param name="filter_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> <output name="normalized_data" file="normalized_data.tsv"/> </test> <!-- The following test has different results on three platform I've tried --> <!-- <test> <param name="data" value="input_data_nobatch.csv" ftype="csv"/> <param name="mode" value="single_batch"/> <param name="wavelet_filter" value="d"/> <param name="filter_length" value="2"/> <param name="k" value="20"/> <param name="alpha" value="0"/> <param name="cutoff" value="0"/> <output name="normalized_data" file="normalized_data_nobatch.tsv"/> </test> --> <test expect_failure="true"> <param name="data" value="na_data.csv" ftype="csv"/> </test> <test expect_failure="true"> <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/> </test> </tests> <help> <![CDATA[ @HELP@ ]]> </help> <citations> <citation type="doi">10.1016/j.aca.2019.02.010</citation> <citation type="doi">10.1007/s11306-021-01839-7</citation> </citations> </tool>