Mercurial > repos > recetox > waveica

annotate waveica.xml @ 4:8b55efc7d117 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit aa8206a01efc1813f2586584782f28a73a17fe86"
author recetox
date Mon, 10 Jan 2022 16:01:35 +0000
parents e3726251a055
children fba892edb9d9
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1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
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2 <description>removal of batch effects for untargeted metabolomics data</description>
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3 <macros>
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4 <import>waveica_macros.xml</import>
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5 </macros>
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6 <expand macro="creator" />
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
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10 </requirements>
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11 <command detect_errors="aggressive"><![CDATA[
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12 Rscript
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13 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
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14
4
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15 #if $batch_correction.mode == "batchwise":
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16 -e 'normalized_data <- waveica(
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17 data = "$data",
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18 wavelet_filter = "$wf.wavelet_filter",
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19 wavelet_length = "$wf.wavelet_length",
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20 k = $k,
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21 t = $batch_correction.t,
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22 t2 = $batch_correction.t2,
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23 alpha = $alpha,
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24 exclude_blanks = $exclude_blanks
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25 )'
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26 #else if $batch_correction.mode == "single_batch":
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27 -e 'normalized_data <- waveica_singlebatch(
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28 data = "$data",
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29 wavelet_filter = "$wf.wavelet_filter",
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30 wavelet_length = "$wf.wavelet_length",
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31 k = $k,
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32 alpha = $alpha,
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33 cutoff = $batch_correction.cutoff,
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34 exclude_blanks = $exclude_blanks
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35 )'
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36 #end if
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37
2
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38 -e 'store_data(normalized_data,"$normalized_data")'
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39 ]]></command>
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41 <inputs>
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42 <expand macro="general_parameters" />
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43 <expand macro="wf" />
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44 <conditional name="batch_correction">
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45 <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]">
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46 <option value="batchwise" selected="true">Multiple batches</option>
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47 <option value="single_batch">Single batch (or no batch information)</option>
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48 </param>
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49 <when value="batchwise">
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50 <expand macro="batchwise_parameters" />
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51 </when>
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52 <when value="single_batch">
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53 <expand macro="singlebatch_parameters" />
2
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54 </when>
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55 </conditional>
4
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56 <expand macro="exclude_blanks" />
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57 </inputs>
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58
4
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59 <expand macro="outputs" />
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61 <tests>
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62 <test>
2
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63 <param name="data" value="input_data.csv" ftype="csv" />
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64 <param name="mode" value="batchwise" />
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65 <param name="wavelet_filter" value="d" />
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66 <param name="filter_length" value="2" />
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67 <param name="k" value="20" />
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68 <param name="t" value="0.05" />
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69 <param name="t2" value="0.05" />
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70 <param name="alpha" value="0" />
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71 <output name="normalized_data" file="normalized_data.tsv" />
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72 </test>
4
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73 <test>
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74 <param name="data" value="input_data_nobatch.csv" ftype="csv" />
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75 <param name="mode" value="single_batch" />
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76 <param name="wavelet_filter" value="d" />
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77 <param name="filter_length" value="2" />
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78 <param name="k" value="20" />
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79 <param name="alpha" value="0" />
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80 <param name="cutoff" value="0" />
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81 <output name="normalized_data" file="normalized_data_nobatch.tsv" />
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82 </test>
2
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83 <test expect_failure="true">
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84 <param name="data" value="na_data.csv" ftype="csv" />
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85 </test>
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86 <test expect_failure="true">
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87 <param name="data" value="incomplete_metadata_data.csv" ftype="csv" />
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88 </test>
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89 </tests>
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90
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91 <help><![CDATA[
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92 **Description**
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93
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94 Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis and independent component analysis.
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95 The WaveICA method uses the time trend of samples over the injection order, decomposes the original data into new multi-scale features, extracts and removes the batch effect resulting in normalized intensities across samples.
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96
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97 The input is an intensity-by-feature table with metadata in the following format:
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98
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99 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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100 | sampleName | class | sampleType | injectionOrder | batch | M85T34 | M86T41 | M86T518 | M86T539 | ... |
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101 +===============+========+============+================+=======+============+==============+=============+=============+=====+
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102 | VT_160120_002 | sample | sample | 1 | 1 | 228520.064 | 35646729.215 | 2386896.979 | 1026645.836 | ... |
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103 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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104 | QC1 | sample | QC | 2 | 1 | 90217.384 | 35735702.457 | 2456290.696 | 1089246.460 | ... |
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105 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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106 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
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107 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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108
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109
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110 + The required columns are **sampleName**, **class**, **sampleType**, **injectionOrder**, and the **features** that you want to normalize.
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111 + The **batch** column is required if batch correction mode is **Multiple batches** and optional otherwise.
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112 + The presence of any additional columns (except features) will result in incorrect batch correction or job failure.
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113 + the input table must not contain missing values. Missing intensities must be filled with 0.
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114 + **sampleType** column accepts three possible values: [QC, sample, blank] (case insensitive).
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115 + **class** column is used to denote a biological group of a sample (e.g., positive/negative species). The column accepts any values.
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116 + the **output** is the same table with corrected feature intensities.
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117
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118 .. rubric:: **Footnotes**
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119 .. [1] for details on wavelet-filter parameters refer to R `wavelets::wt.filter <https://www.rdocumentation.org/packages/wavelets/versions/0.3-0.2/topics/wt.filter>`_;
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120 .. [2] when using 'Multiple batches', please cite the WaveICA (2019) paper; else, cite WaveICA 2.0 (2021) paper;
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121
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122
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123 ]]></help>
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124
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125 <citations>
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126 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
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127 <citation type="doi">10.1007/s11306-021-01839-7</citation>
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128 </citations>
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129
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130 </tool>