Mercurial > repos > recetox > waveica

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
author recetox
date Fri, 04 Jul 2025 09:43:22 +0000
parents 6fc9f6dbcef5
children
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10
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy10" profile="23.0">
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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>macros.xml</import>
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5 </macros>
2
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6 <expand macro="annotation"/>
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7 <expand macro="creator"/>
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8
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
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11 <requirement type="package" version="8.0.0">r-arrow</requirement>
10
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12 <requirement type="package" version="1.0.10">r-dplyr</requirement>
0
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13 </requirements>
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14 <command detect_errors="aggressive"><![CDATA[
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15 Rscript -e "source('${__tool_directory__}/waveica_wrapper.R');
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16 normalized_data <-
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17 #if $batch_correction.mode == 'batchwise':
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18 waveica(
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19 data_matrix_file = '$data_matrix',
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20 sample_metadata_file = '$sample_metadata',
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21 ft_ext = '$data_matrix.ext',
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22 mt_ext = '$sample_metadata.ext',
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23 wavelet_filter = '$wf.wavelet_filter',
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24 wavelet_length = '$wf.wavelet_length',
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25 k = $k,
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26 t = $batch_correction.t,
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27 t2 = $batch_correction.t2,
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28 alpha = $alpha,
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29 exclude_blanks = $exclude_blanks,
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30 transpose = $transpose_feature_table
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31 )
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32 #else:
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33 waveica_singlebatch(
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34 data_matrix_file = '$data_matrix',
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35 sample_metadata_file = '$sample_metadata',
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36 ft_ext = '$data_matrix.ext',
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37 mt_ext = '$sample_metadata.ext',
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38 wavelet_filter = '$wf.wavelet_filter',
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39 wavelet_length = '$wf.wavelet_length',
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40 k = $k,
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41 alpha = $alpha,
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42 cutoff = $batch_correction.cutoff,
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43 exclude_blanks = $exclude_blanks
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44 transpose = $transpose_feature_table
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45 )
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46 #end if
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47 ;store_data(normalized_data, '$normalized_data', '$data_matrix.ext')"
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48 ]]></command>
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49
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50 <inputs>
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51 <param name="data_matrix" type="data" label="Feature table" format="csv,tsv,tabular,parquet" help="Table of measured features for each sample."/>
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52 <param name="sample_metadata" label="Input sample metadata" type="data" format="csv,tsv,tabular,parquet" help="Table with sample information (e.g., sample name, class, batch, injection order) for each sample." />
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53 <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
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54 truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
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55 <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>
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56 <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"/>
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57 <expand macro="wf"/>
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58 <conditional name="batch_correction">
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59 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
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60 inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
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61 requires no batch information [2]">
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62 <option value="batchwise" selected="true">Multiple batches</option>
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63 <option value="single_batch">Single batch (or no batch information)</option>
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64 </param>
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65 <when value="batchwise">
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66 <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"/>
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67 <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"/>
0
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68 </when>
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69 <when value="single_batch">
9
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70 <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"/>
0
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71 </when>
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72 </conditional>
9
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73 <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
0
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74 </inputs>
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75
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76 <expand macro="outputs"/>
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77
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78 <tests>
10
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79 <test><!-- TEST 1: CSV input -->
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80 <param name="data_matrix" value="data_matrix.csv" ftype="csv"/>
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81 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
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82 <param name="alpha" value="0"/>
0
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83 <param name="k" value="20"/>
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84 <conditional name="wf">
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85 <param name="wavelet_filter" value="d"/>
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86 <param name="wavelet_length" value="2"/>
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87 </conditional>
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88 <conditional name="batch_correction">
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89 <param name="mode" value="batchwise"/>
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90 <param name="t" value="0.05"/>
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91 <param name="t2" value="0.05"/>
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92 </conditional>
10
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93 <output name="normalized_data" file="test1_output.csv" ftype="csv"/>
1
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94 </test>
10
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95 <test><!-- TEST 2: TSV input -->
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96 <param name="data_matrix" value="data_matrix.tsv" ftype="tabular"/>
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97 <param name="sample_metadata" value="sample_metadata.tsv" ftype="tabular"/>
9
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98 <param name="alpha" value="0"/>
1
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99 <param name="k" value="20"/>
9
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100 <conditional name="wf">
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101 <param name="wavelet_filter" value="d"/>
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102 <param name="wavelet_length" value="2"/>
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103 </conditional>
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104 <conditional name="batch_correction">
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105 <param name="mode" value="batchwise"/>
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106 <param name="t" value="0.05"/>
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107 <param name="t2" value="0.05"/>
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108 </conditional>
7
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109 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
0
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110 </test>
10
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111 <test><!-- TEST 3: Parquet input -->
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112 <param name="data_matrix" value="data_matrix.parquet" ftype="parquet"/>
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113 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
9
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114 <param name="alpha" value="0"/>
1
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115 <param name="k" value="20"/>
9
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116 <conditional name="wf">
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117 <param name="wavelet_filter" value="d"/>
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118 <param name="wavelet_length" value="2"/>
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119 </conditional>
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120 <conditional name="batch_correction">
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121 <param name="mode" value="batchwise"/>
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122 <param name="t" value="0.05"/>
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123 <param name="t2" value="0.05"/>
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124 </conditional>
10
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125 <output name="normalized_data" file="test3_output.parquet" compare="sim_size" delta="200" ftype="parquet"/>
1
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126 </test>
10
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127 <test expect_failure="true"><!-- TEST 4: NA data should fail -->
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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128 <param name="data_matrix" value="na_data.csv" ftype="csv"/>
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129 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
1
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130 </test>
10
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diff changeset
131 <test expect_failure="true"><!-- TEST 5: Incomplete metadata should fail -->
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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132 <param name="data_matrix" value="data_matrix.csv" ftype="csv"/>
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133 <param name="sample_metadata" value="incomplete_metadata_data.csv" ftype="csv"/>
1
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134 </test>
10
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135
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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136 <test><!-- TEST 6 -->
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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137 <param name="data_matrix" value="feature_table_transpose_version.parquet" ftype="parquet"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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138 <param name="sample_metadata" value="sample_metadata.parquet" ftype="parquet"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
139 <param name="transpose_feature_table" value="TRUE"/>
4
425c0494ec2d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 84de3bc96ad2859d87c70ba94d8ceb0b2bc2a0da
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140 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
2
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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141 </test>
10
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diff changeset
142 <test><!-- TEST 7 -->
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diff changeset
143 <param name="data_matrix" value="feature_table_transpose_version.csv" ftype="csv"/>
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diff changeset
144 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
145 <param name="transpose_feature_table" value="TRUE"/>
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146 <output name="normalized_data" file="normalized_data.csv" ftype="csv"/>
7
1a2aeb8137bf planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 013d7c85fa9d77b8a27d194b350cd6b2d127a80f
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147 </test>
10
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diff changeset
148 <test><!-- TEST 8 -->
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149 <param name="data_matrix" value="feature_table_transpose_version.parquet" ftype="parquet"/>
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150 <param name="sample_metadata" value="sample_metadata.parquet" ftype="parquet"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
151 <param name="transpose_feature_table" value="TRUE"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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152 <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
7
1a2aeb8137bf planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 013d7c85fa9d77b8a27d194b350cd6b2d127a80f
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153 </test>
10
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
154 <test><!-- TEST 9 -->
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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155 <param name="data_matrix" value="feature_table_transpose_version.csv" ftype="csv"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
156 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
821062fc5782 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 2b8b1dcb2947c6503fd4f82904df708e4f88ea1d
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diff changeset
157 <param name="transpose_feature_table" value="TRUE"/>
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diff changeset
158 <output name="normalized_data" file="test10_output1.csv" ftype="csv"/>
0
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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159 </test>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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160 </tests>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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161
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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162 <help>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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163 <![CDATA[
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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164 @HELP@
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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165 ]]>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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166 </help>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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167
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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168 <citations>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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169 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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170 <citation type="doi">10.1007/s11306-021-01839-7</citation>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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171 </citations>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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172
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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173 </tool>