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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 013d7c85fa9d77b8a27d194b350cd6b2d127a80f
author recetox
date Thu, 06 Jun 2024 12:25:05 +0000
parents e424fa636281
children
comparison
equal deleted inserted replaced
6:071a424241ec 7:1a2aeb8137bf
1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy6" profile="21.09"> 1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy7" profile="21.09">
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"/>
49 cutoff = $batch_correction.cutoff, 49 cutoff = $batch_correction.cutoff,
50 exclude_blanks = $exclude_blanks 50 exclude_blanks = $exclude_blanks
51 )' 51 )'
52 #end if 52 #end if
53 53
54 -e 'store_data(normalized_data, "$normalized_data", "$input_num.data.ext")' 54 -e 'store_data(normalized_data, "$normalized_data", "$metadata", "$input_num.data.ext", $keep_two_output)'
55 ]]></command> 55 ]]></command>
56 56
57 <inputs> 57 <inputs>
58 <conditional name="input_num"> 58 <conditional name="input_num">
59 <param name="input_choice" type="select" label="Choose input files:"> 59 <param name="input_choice" type="select" label="Choose input files:">
60 <option value="1" selected="true">1</option> 60 <option value="1" selected="true">1: intensity-by-feature table with metadata</option>
61 <option value="2">2</option> 61 <option value="2">2: intensity-by-feature table and metadata table separately</option>
62 </param> 62 </param>
63 <when value="1"> 63 <when value="1">
64 <expand macro="input_data"/> 64 <expand macro="input_data"/>
65 </when> 65 </when>
66 <when value="2"> 66 <when value="2">
87 <when value="single_batch"> 87 <when value="single_batch">
88 <expand macro="singlebatch_parameters"/> 88 <expand macro="singlebatch_parameters"/>
89 </when> 89 </when>
90 </conditional> 90 </conditional>
91 <expand macro="exclude_blanks"/> 91 <expand macro="exclude_blanks"/>
92 <expand macro="split_output"/>
92 </inputs> 93 </inputs>
93 94
94 <expand macro="outputs"/> 95 <expand macro="outputs"/>
95 96
96 <tests> 97 <tests>
97 <test><!-- TEST 1 --> 98 <test expect_num_outputs="1"><!-- TEST 1 -->
98 <param name="data" value="input_data.csv" ftype="csv"/> 99 <param name="data" value="input_data.csv" ftype="csv"/>
99 <param name="mode" value="batchwise"/> 100 <param name="mode" value="batchwise"/>
100 <param name="wavelet_filter" value="d"/> 101 <param name="wavelet_filter" value="d"/>
101 <param name="wavelet_length" value="2"/> 102 <param name="wavelet_length" value="2"/>
102 <param name="k" value="20"/> 103 <param name="k" value="20"/>
103 <param name="t" value="0.05"/> 104 <param name="t" value="0.05"/>
104 <param name="t2" value="0.05"/> 105 <param name="t2" value="0.05"/>
105 <param name="alpha" value="0"/> 106 <param name="alpha" value="0"/>
106 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> 107 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
107 </test> 108 </test>
108 <test><!-- TEST 2 --> 109 <test expect_num_outputs="1"><!-- TEST 2 -->
109 <param name="data" value="input_data.tsv" ftype="tsv"/> 110 <param name="data" value="input_data.tsv" ftype="tsv"/>
110 <param name="mode" value="batchwise"/> 111 <param name="mode" value="batchwise"/>
111 <param name="wavelet_filter" value="d"/> 112 <param name="wavelet_filter" value="d"/>
112 <param name="wavelet_length" value="2"/> 113 <param name="wavelet_length" value="2"/>
113 <param name="k" value="20"/> 114 <param name="k" value="20"/>
114 <param name="t" value="0.05"/> 115 <param name="t" value="0.05"/>
115 <param name="t2" value="0.05"/> 116 <param name="t2" value="0.05"/>
116 <param name="alpha" value="0"/> 117 <param name="alpha" value="0"/>
117 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> 118 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
118 </test> 119 </test>
119 <test><!-- TEST 3 --> 120 <test expect_num_outputs="1"><!-- TEST 3 -->
120 <param name="data" value="input_data.parquet" ftype="parquet"/> 121 <param name="data" value="input_data.parquet" ftype="parquet"/>
121 <param name="mode" value="batchwise"/> 122 <param name="mode" value="batchwise"/>
122 <param name="wavelet_filter" value="d"/> 123 <param name="wavelet_filter" value="d"/>
123 <param name="wavelet_length" value="2"/> 124 <param name="wavelet_length" value="2"/>
124 <param name="k" value="20"/> 125 <param name="k" value="20"/>
125 <param name="t" value="0.05"/> 126 <param name="t" value="0.05"/>
126 <param name="t2" value="0.05"/> 127 <param name="t2" value="0.05"/>
127 <param name="alpha" value="0"/> 128 <param name="alpha" value="0"/>
128 <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/> 129 <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
129 </test> 130 </test>
130 <test><!-- TEST 4 --> 131 <test expect_num_outputs="1"><!-- TEST 4 -->
131 <param name="input_choice" value="2"/> 132 <param name="input_choice" value="2"/>
132 <param name="data" value="feature_table.csv" ftype="csv"/> 133 <param name="data" value="feature_table.csv" ftype="csv"/>
133 <param name="metadata" value="metadata.csv" ftype="csv"/> 134 <param name="metadata" value="metadata.csv" ftype="csv"/>
134 <param name="mode" value="batchwise"/> 135 <param name="mode" value="batchwise"/>
135 <param name="wavelet_filter" value="d"/> 136 <param name="wavelet_filter" value="d"/>
136 <param name="wavelet_length" value="2"/> 137 <param name="wavelet_length" value="2"/>
137 <param name="k" value="20"/> 138 <param name="k" value="20"/>
138 <param name="t" value="0.05"/> 139 <param name="t" value="0.05"/>
139 <param name="t2" value="0.05"/> 140 <param name="t2" value="0.05"/>
140 <param name="alpha" value="0"/> 141 <param name="alpha" value="0"/>
141 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> 142 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
142 </test> 143 </test>
143 <test><!-- TEST 5 --> 144 <test expect_num_outputs="1"><!-- TEST 5 -->
144 <param name="input_choice" value="2"/> 145 <param name="input_choice" value="2"/>
145 <param name="data" value="feature_table.tsv" ftype="tsv"/> 146 <param name="data" value="feature_table.tsv" ftype="tsv"/>
146 <param name="metadata" value="metadata.tsv" ftype="tsv"/> 147 <param name="metadata" value="metadata.tsv" ftype="tsv"/>
147 <param name="mode" value="batchwise"/> 148 <param name="mode" value="batchwise"/>
148 <param name="wavelet_filter" value="d"/> 149 <param name="wavelet_filter" value="d"/>
149 <param name="wavelet_length" value="2"/> 150 <param name="wavelet_length" value="2"/>
150 <param name="k" value="20"/> 151 <param name="k" value="20"/>
151 <param name="t" value="0.05"/> 152 <param name="t" value="0.05"/>
152 <param name="t2" value="0.05"/> 153 <param name="t2" value="0.05"/>
153 <param name="alpha" value="0"/> 154 <param name="alpha" value="0"/>
154 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> 155 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
155 </test> 156 </test>
156 <test><!-- TEST 6 --> 157 <test expect_num_outputs="1"><!-- TEST 6 -->
157 <param name="input_choice" value="2"/> 158 <param name="input_choice" value="2"/>
158 <param name="data" value="feature_table.parquet" ftype="parquet"/> 159 <param name="data" value="feature_table.parquet" ftype="parquet"/>
159 <param name="metadata" value="metadata.csv" ftype="csv"/> 160 <param name="metadata" value="metadata.csv" ftype="csv"/>
160 <param name="mode" value="batchwise"/> 161 <param name="mode" value="batchwise"/>
161 <param name="wavelet_filter" value="d"/> 162 <param name="wavelet_filter" value="d"/>
164 <param name="t" value="0.05"/> 165 <param name="t" value="0.05"/>
165 <param name="t2" value="0.05"/> 166 <param name="t2" value="0.05"/>
166 <param name="alpha" value="0"/> 167 <param name="alpha" value="0"/>
167 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/> 168 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
168 </test> 169 </test>
169 <test><!-- TEST 7 --> 170 <test expect_num_outputs="1"><!-- TEST 7 -->
170 <param name="input_choice" value="2"/> 171 <param name="input_choice" value="2"/>
171 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/> 172 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
172 <param name="metadata" value="metadata.parquet" ftype="parquet"/> 173 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
173 <param name="transpose_feature_table" value="TRUE"/> 174 <param name="transpose_feature_table" value="TRUE"/>
174 <param name="mode" value="batchwise"/> 175 <param name="mode" value="batchwise"/>
178 <param name="t" value="0.05"/> 179 <param name="t" value="0.05"/>
179 <param name="t2" value="0.05"/> 180 <param name="t2" value="0.05"/>
180 <param name="alpha" value="0"/> 181 <param name="alpha" value="0"/>
181 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/> 182 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
182 </test> 183 </test>
183 <test><!-- TEST 8 --> 184 <test expect_num_outputs="1"><!-- TEST 8 -->
184 <param name="input_choice" value="2"/> 185 <param name="input_choice" value="2"/>
185 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/> 186 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
186 <param name="metadata" value="metadata.csv" ftype="csv"/> 187 <param name="metadata" value="metadata.csv" ftype="csv"/>
187 <param name="transpose_feature_table" value="TRUE"/> 188 <param name="transpose_feature_table" value="TRUE"/>
188 <param name="mode" value="batchwise"/> 189 <param name="mode" value="batchwise"/>
190 <param name="wavelet_length" value="2"/> 191 <param name="wavelet_length" value="2"/>
191 <param name="k" value="20"/> 192 <param name="k" value="20"/>
192 <param name="t" value="0.05"/> 193 <param name="t" value="0.05"/>
193 <param name="t2" value="0.05"/> 194 <param name="t2" value="0.05"/>
194 <param name="alpha" value="0"/> 195 <param name="alpha" value="0"/>
195 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> 196 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
196 </test> 197 </test>
197 <!-- The following test has different results on three platform I've tried --> 198 <!-- The following test has different results on three platform I've tried -->
198 <!-- <test> 199 <!-- <test>
199 <param name="data" value="input_data_nobatch.csv" ftype="csv"/> 200 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
200 <param name="mode" value="single_batch"/> 201 <param name="mode" value="single_batch"/>
203 <param name="k" value="20"/> 204 <param name="k" value="20"/>
204 <param name="alpha" value="0"/> 205 <param name="alpha" value="0"/>
205 <param name="cutoff" value="0"/> 206 <param name="cutoff" value="0"/>
206 <output name="normalized_data" file="normalized_data_nobatch.tsv"/> 207 <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
207 </test> --> 208 </test> -->
208 <test expect_failure="true"> 209 <test expect_num_outputs="2"><!-- TEST 9 -->
210 <param name="input_choice" value="2"/>
211 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
212 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
213 <param name="transpose_feature_table" value="TRUE"/>
214 <param name="mode" value="batchwise"/>
215 <param name="wavelet_filter" value="d"/>
216 <param name="wavelet_length" value="2"/>
217 <param name="k" value="20"/>
218 <param name="t" value="0.05"/>
219 <param name="t2" value="0.05"/>
220 <param name="alpha" value="0"/>
221 <param name="keep_two_output" value="TRUE"/>
222 <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
223 <output name="metadata" file="test9_output2.parquet" ftype="parquet"/>
224 </test>
225 <test expect_num_outputs="2"><!-- TEST 10 -->
226 <param name="input_choice" value="2"/>
227 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
228 <param name="metadata" value="metadata.csv" ftype="csv"/>
229 <param name="transpose_feature_table" value="TRUE"/>
230 <param name="mode" value="batchwise"/>
231 <param name="wavelet_filter" value="d"/>
232 <param name="wavelet_length" value="2"/>
233 <param name="k" value="20"/>
234 <param name="t" value="0.05"/>
235 <param name="t2" value="0.05"/>
236 <param name="alpha" value="0"/>
237 <param name="keep_two_output" value="TRUE"/>
238 <output name="normalized_data" file="test10_output1.tsv" ftype="tabular"/>
239 <output name="metadata" file="test10_output2.tsv" ftype="tabular"/>
240 </test>
241 <test expect_failure="true"><!-- TEST 11 -->
209 <param name="data" value="na_data.csv" ftype="csv"/> 242 <param name="data" value="na_data.csv" ftype="csv"/>
210 </test> 243 </test>
211 <test expect_failure="true"> 244 <test expect_failure="true"><!-- TEST 12 -->
212 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/> 245 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
213 </test> 246 </test>
214 </tests> 247 </tests>
215 248
216 <help> 249 <help>