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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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9:6fc9f6dbcef5 10:821062fc5782
1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy9" profile="23.0"> 1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy10" profile="23.0">
2 <description>removal of batch effects for untargeted metabolomics data</description> 2 <description>removal of batch effects for untargeted metabolomics data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="annotation"/> 6 <expand macro="annotation"/>
7 <expand macro="creator"/> 7 <expand macro="creator"/>
8 8
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
11 <requirement type="package" version="8.0.0">r-arrow</requirement> 11 <requirement type="package" version="8.0.0">r-arrow</requirement>
12 <requirement type="package" version="1.0.10">r-dplyr</requirement>
12 </requirements> 13 </requirements>
13 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
14 Rscript 15 Rscript -e "source('${__tool_directory__}/waveica_wrapper.R');
15 -e 'source("${__tool_directory__}/waveica_wrapper.R")' 16 normalized_data <-
16 17 #if $batch_correction.mode == 'batchwise':
17 #if $batch_correction.mode == "batchwise": 18 waveica(
18 -e 'normalized_data <- waveica( 19 data_matrix_file = '$data_matrix',
19 file = "$input_num.data", 20 sample_metadata_file = '$sample_metadata',
20 #if $input_num.input_choice == "2": 21 ft_ext = '$data_matrix.ext',
21 metadata = "$input_num.metadata", 22 mt_ext = '$sample_metadata.ext',
22 ext = "$input_num.data.ext,$input_num.metadata.ext", 23 wavelet_filter = '$wf.wavelet_filter',
23 transpose = $input_num.transpose_feature_table, 24 wavelet_length = '$wf.wavelet_length',
24 #else:
25 ext = "$input_num.data.ext",
26 #end if
27 wavelet_filter = "$wf.wavelet_filter",
28 wavelet_length = "$wf.wavelet_length",
29 k = $k, 25 k = $k,
30 t = $batch_correction.t, 26 t = $batch_correction.t,
31 t2 = $batch_correction.t2, 27 t2 = $batch_correction.t2,
32 alpha = $alpha, 28 alpha = $alpha,
33 exclude_blanks = $exclude_blanks 29 exclude_blanks = $exclude_blanks,
34 )' 30 transpose = $transpose_feature_table
35 #else if $batch_correction.mode == "single_batch": 31 )
36 -e 'normalized_data <- waveica_singlebatch( 32 #else:
37 file = "$input_num.data", 33 waveica_singlebatch(
38 #if $input_num.input_choice == "2": 34 data_matrix_file = '$data_matrix',
39 metadata = "$input_num.metadata", 35 sample_metadata_file = '$sample_metadata',
40 ext = "$input_num.data.ext,$input_num.metadata.ext", 36 ft_ext = '$data_matrix.ext',
41 transpose = $input_num.transpose_feature_table, 37 mt_ext = '$sample_metadata.ext',
42 #else: 38 wavelet_filter = '$wf.wavelet_filter',
43 ext = "$input_num.data.ext", 39 wavelet_length = '$wf.wavelet_length',
44 #end if
45 wavelet_filter = "$wf.wavelet_filter",
46 wavelet_length = "$wf.wavelet_length",
47 k = $k, 40 k = $k,
48 alpha = $alpha, 41 alpha = $alpha,
49 cutoff = $batch_correction.cutoff, 42 cutoff = $batch_correction.cutoff,
50 exclude_blanks = $exclude_blanks 43 exclude_blanks = $exclude_blanks
51 )' 44 transpose = $transpose_feature_table
52 #end if 45 )
53 46 #end if
54 -e 'store_data(normalized_data, "$normalized_data", "$metadata", "$input_num.data.ext", $keep_two_output)' 47 ;store_data(normalized_data, '$normalized_data', '$data_matrix.ext')"
55 ]]></command> 48 ]]></command>
56 49
57 <inputs> 50 <inputs>
58 <conditional name="input_num"> 51 <param name="data_matrix" type="data" label="Feature table" format="csv,tsv,tabular,parquet" help="Table of measured features for each sample."/>
59 <param name="input_choice" type="select" label="Choose input files:"> 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." />
60 <option value="1" selected="true">1: intensity-by-feature table with metadata</option> 53 <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
61 <option value="2">2: intensity-by-feature table and metadata table separately</option>
62 </param>
63 <when value="1">
64 <expand macro="input_data"/>
65 </when>
66 <when value="2">
67 <expand macro="input_data"/>
68 <param name="metadata" label="Input metadata" type="data" format="csv,tsv,tabular,parquet" help="" />
69 <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
70 truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." /> 54 truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
71 </when>
72 </conditional>
73 <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/> 55 <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>
74 <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"/> 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"/>
75 <expand macro="wf"/> 57 <expand macro="wf"/>
76 <conditional name="batch_correction"> 58 <conditional name="batch_correction">
77 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account 59 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
87 <when value="single_batch"> 69 <when value="single_batch">
88 <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"/> 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"/>
89 </when> 71 </when>
90 </conditional> 72 </conditional>
91 <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" /> 73 <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
92 <expand macro="split_output"/>
93 </inputs> 74 </inputs>
94 75
95 <expand macro="outputs"/> 76 <expand macro="outputs"/>
96 77
97 <tests> 78 <tests>
98 <test expect_num_outputs="1"><!-- TEST 1 --> 79 <test><!-- TEST 1: CSV input -->
99 <conditional name="input_num"> 80 <param name="data_matrix" value="data_matrix.csv" ftype="csv"/>
100 <param name="data" value="input_data.csv" ftype="csv"/> 81 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
82 <param name="alpha" value="0"/>
83 <param name="k" value="20"/>
84 <conditional name="wf">
85 <param name="wavelet_filter" value="d"/>
86 <param name="wavelet_length" value="2"/>
101 </conditional> 87 </conditional>
88 <conditional name="batch_correction">
89 <param name="mode" value="batchwise"/>
90 <param name="t" value="0.05"/>
91 <param name="t2" value="0.05"/>
92 </conditional>
93 <output name="normalized_data" file="test1_output.csv" ftype="csv"/>
94 </test>
95 <test><!-- TEST 2: TSV input -->
96 <param name="data_matrix" value="data_matrix.tsv" ftype="tabular"/>
97 <param name="sample_metadata" value="sample_metadata.tsv" ftype="tabular"/>
102 <param name="alpha" value="0"/> 98 <param name="alpha" value="0"/>
103 <param name="k" value="20"/> 99 <param name="k" value="20"/>
104 <conditional name="wf"> 100 <conditional name="wf">
105 <param name="wavelet_filter" value="d"/> 101 <param name="wavelet_filter" value="d"/>
106 <param name="wavelet_length" value="2"/> 102 <param name="wavelet_length" value="2"/>
110 <param name="t" value="0.05"/> 106 <param name="t" value="0.05"/>
111 <param name="t2" value="0.05"/> 107 <param name="t2" value="0.05"/>
112 </conditional> 108 </conditional>
113 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/> 109 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
114 </test> 110 </test>
115 <test expect_num_outputs="1"><!-- TEST 2 --> 111 <test><!-- TEST 3: Parquet input -->
116 <conditional name="input_num"> 112 <param name="data_matrix" value="data_matrix.parquet" ftype="parquet"/>
117 <param name="data" value="input_data.tsv" ftype="tsv"/> 113 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
118 </conditional>
119 <param name="alpha" value="0"/> 114 <param name="alpha" value="0"/>
120 <param name="k" value="20"/> 115 <param name="k" value="20"/>
121 <conditional name="wf"> 116 <conditional name="wf">
122 <param name="wavelet_filter" value="d"/> 117 <param name="wavelet_filter" value="d"/>
123 <param name="wavelet_length" value="2"/> 118 <param name="wavelet_length" value="2"/>
125 <conditional name="batch_correction"> 120 <conditional name="batch_correction">
126 <param name="mode" value="batchwise"/> 121 <param name="mode" value="batchwise"/>
127 <param name="t" value="0.05"/> 122 <param name="t" value="0.05"/>
128 <param name="t2" value="0.05"/> 123 <param name="t2" value="0.05"/>
129 </conditional> 124 </conditional>
130 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/> 125 <output name="normalized_data" file="test3_output.parquet" compare="sim_size" delta="200" ftype="parquet"/>
131 </test> 126 </test>
132 <test expect_num_outputs="1"><!-- TEST 3 --> 127 <test expect_failure="true"><!-- TEST 4: NA data should fail -->
133 <conditional name="input_num"> 128 <param name="data_matrix" value="na_data.csv" ftype="csv"/>
134 <param name="data" value="input_data.parquet" ftype="parquet"/> 129 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
135 </conditional>
136 <param name="k" value="20"/>
137 <param name="alpha" value="0"/>
138 <conditional name="wf">
139 <param name="wavelet_filter" value="d"/>
140 <param name="wavelet_length" value="2"/>
141 </conditional>
142 <conditional name="batch_correction">
143 <param name="mode" value="batchwise"/>
144 <param name="t" value="0.05"/>
145 <param name="t2" value="0.05"/>
146 </conditional>
147 <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
148 </test> 130 </test>
149 <test expect_num_outputs="1"><!-- TEST 4 --> 131 <test expect_failure="true"><!-- TEST 5: Incomplete metadata should fail -->
150 <conditional name="input_num"> 132 <param name="data_matrix" value="data_matrix.csv" ftype="csv"/>
151 <param name="input_choice" value="2"/> 133 <param name="sample_metadata" value="incomplete_metadata_data.csv" ftype="csv"/>
152 <param name="data" value="feature_table.csv" ftype="csv"/>
153 <param name="metadata" value="metadata.csv" ftype="csv"/>
154 </conditional>
155 <param name="alpha" value="0"/>
156 <param name="k" value="20"/>
157 <conditional name="wf">
158 <param name="wavelet_filter" value="d"/>
159 <param name="wavelet_length" value="2"/>
160 </conditional>
161 <conditional name="batch_correction">
162 <param name="mode" value="batchwise"/>
163 <param name="t" value="0.05"/>
164 <param name="t2" value="0.05"/>
165 </conditional>
166 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
167 </test> 134 </test>
168 <test expect_num_outputs="1"><!-- TEST 5 --> 135
169 <conditional name="input_num"> 136 <test><!-- TEST 6 -->
170 <param name="input_choice" value="2"/> 137 <param name="data_matrix" value="feature_table_transpose_version.parquet" ftype="parquet"/>
171 <param name="data" value="feature_table.tsv" ftype="tabular"/> 138 <param name="sample_metadata" value="sample_metadata.parquet" ftype="parquet"/>
172 <param name="metadata" value="metadata.tsv" ftype="tabular"/> 139 <param name="transpose_feature_table" value="TRUE"/>
173 </conditional>
174 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
175 </test>
176 <test expect_num_outputs="1"><!-- TEST 6 -->
177 <conditional name="input_num">
178 <param name="input_choice" value="2"/>
179 <param name="data" value="feature_table.parquet" ftype="parquet"/>
180 <param name="metadata" value="metadata.csv" ftype="csv"/>
181 </conditional>
182 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/> 140 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
183 </test> 141 </test>
184 <test expect_num_outputs="1"><!-- TEST 7 --> 142 <test><!-- TEST 7 -->
185 <conditional name="input_num"> 143 <param name="data_matrix" value="feature_table_transpose_version.csv" ftype="csv"/>
186 <param name="input_choice" value="2"/> 144 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
187 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/> 145 <param name="transpose_feature_table" value="TRUE"/>
188 <param name="metadata" value="metadata.parquet" ftype="parquet"/> 146 <output name="normalized_data" file="normalized_data.csv" ftype="csv"/>
189 <param name="transpose_feature_table" value="TRUE"/>
190 </conditional>
191 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
192 </test> 147 </test>
193 <test expect_num_outputs="1"><!-- TEST 8 --> 148 <test><!-- TEST 8 -->
194 <conditional name="input_num"> 149 <param name="data_matrix" value="feature_table_transpose_version.parquet" ftype="parquet"/>
195 <param name="input_choice" value="2"/> 150 <param name="sample_metadata" value="sample_metadata.parquet" ftype="parquet"/>
196 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/> 151 <param name="transpose_feature_table" value="TRUE"/>
197 <param name="metadata" value="metadata.csv" ftype="csv"/> 152 <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
198 <param name="transpose_feature_table" value="TRUE"/>
199 </conditional>
200 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
201 </test> 153 </test>
202 <test expect_num_outputs="2"><!-- TEST 9 --> 154 <test><!-- TEST 9 -->
203 <conditional name="input_num"> 155 <param name="data_matrix" value="feature_table_transpose_version.csv" ftype="csv"/>
204 <param name="input_choice" value="2"/> 156 <param name="sample_metadata" value="sample_metadata.csv" ftype="csv"/>
205 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/> 157 <param name="transpose_feature_table" value="TRUE"/>
206 <param name="metadata" value="metadata.parquet" ftype="parquet"/> 158 <output name="normalized_data" file="test10_output1.csv" ftype="csv"/>
207 <param name="transpose_feature_table" value="TRUE"/>
208 </conditional>
209 <param name="keep_two_output" value="TRUE"/>
210 <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
211 <output name="metadata" file="test9_output2.parquet" ftype="parquet"/>
212 </test>
213 <test expect_num_outputs="2"><!-- TEST 10 -->
214 <conditional name="input_num">
215 <param name="input_choice" value="2"/>
216 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
217 <param name="metadata" value="metadata.csv" ftype="csv"/>
218 <param name="transpose_feature_table" value="TRUE"/>
219 </conditional>
220 <param name="keep_two_output" value="TRUE"/>
221 <output name="normalized_data" file="test10_output1.tsv" ftype="tabular"/>
222 <output name="metadata" file="test10_output2.tsv" ftype="tabular"/>
223 </test>
224 <test expect_failure="true"><!-- TEST 11 -->
225 <conditional name="input_num">
226 <param name="data" value="na_data.csv" ftype="csv"/>
227 </conditional>
228 </test>
229 <test expect_failure="true"><!-- TEST 12 -->
230 <conditional name="input_num">
231 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
232 </conditional>
233 </test> 159 </test>
234 </tests> 160 </tests>
235 161
236 <help> 162 <help>
237 <![CDATA[ 163 <![CDATA[