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comparison waveica.xml @ 4:425c0494ec2d draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 84de3bc96ad2859d87c70ba94d8ceb0b2bc2a0da
author recetox
date Tue, 07 May 2024 12:49:20 +0000
parents dbbedb14b44c
children e424fa636281
comparison
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3:dbbedb14b44c 4:425c0494ec2d
1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy4" python_template_version="3.5"> 1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy5" 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"/>
101 <param name="wavelet_length" value="2"/> 101 <param name="wavelet_length" value="2"/>
102 <param name="k" value="20"/> 102 <param name="k" value="20"/>
103 <param name="t" value="0.05"/> 103 <param name="t" value="0.05"/>
104 <param name="t2" value="0.05"/> 104 <param name="t2" value="0.05"/>
105 <param name="alpha" value="0"/> 105 <param name="alpha" value="0"/>
106 <output name="normalized_data" file="normalized_data.csv"/> 106 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
107 </test> 107 </test>
108 <test><!-- TEST 2 --> 108 <test><!-- TEST 2 -->
109 <param name="data" value="input_data.tsv" ftype="tsv"/> 109 <param name="data" value="input_data.tsv" ftype="tsv"/>
110 <param name="mode" value="batchwise"/> 110 <param name="mode" value="batchwise"/>
111 <param name="wavelet_filter" value="d"/> 111 <param name="wavelet_filter" value="d"/>
112 <param name="wavelet_length" value="2"/> 112 <param name="wavelet_length" value="2"/>
113 <param name="k" value="20"/> 113 <param name="k" value="20"/>
114 <param name="t" value="0.05"/> 114 <param name="t" value="0.05"/>
115 <param name="t2" value="0.05"/> 115 <param name="t2" value="0.05"/>
116 <param name="alpha" value="0"/> 116 <param name="alpha" value="0"/>
117 <output name="normalized_data" file="normalized_data.tsv"/> 117 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
118 </test> 118 </test>
119 <test><!-- TEST 3 --> 119 <test><!-- TEST 3 -->
120 <param name="data" value="input_data.parquet" ftype="parquet"/> 120 <param name="data" value="input_data.parquet" ftype="parquet"/>
121 <param name="mode" value="batchwise"/> 121 <param name="mode" value="batchwise"/>
122 <param name="wavelet_filter" value="d"/> 122 <param name="wavelet_filter" value="d"/>
123 <param name="wavelet_length" value="2"/> 123 <param name="wavelet_length" value="2"/>
124 <param name="k" value="20"/> 124 <param name="k" value="20"/>
125 <param name="t" value="0.05"/> 125 <param name="t" value="0.05"/>
126 <param name="t2" value="0.05"/> 126 <param name="t2" value="0.05"/>
127 <param name="alpha" value="0"/> 127 <param name="alpha" value="0"/>
128 <output name="normalized_data" file="normalized_data.parquet"/> 128 <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
129 </test> 129 </test>
130 <test><!-- TEST 4 --> 130 <test><!-- TEST 4 -->
131 <param name="input_choice" value="2"/> 131 <param name="input_choice" value="2"/>
132 <param name="data" value="feature_table.csv" ftype="csv"/> 132 <param name="data" value="feature_table.csv" ftype="csv"/>
133 <param name="metadata" value="metadata.csv" ftype="csv"/> 133 <param name="metadata" value="metadata.csv" ftype="csv"/>
136 <param name="wavelet_length" value="2"/> 136 <param name="wavelet_length" value="2"/>
137 <param name="k" value="20"/> 137 <param name="k" value="20"/>
138 <param name="t" value="0.05"/> 138 <param name="t" value="0.05"/>
139 <param name="t2" value="0.05"/> 139 <param name="t2" value="0.05"/>
140 <param name="alpha" value="0"/> 140 <param name="alpha" value="0"/>
141 <output name="normalized_data" file="normalized_data.csv"/> 141 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
142 </test> 142 </test>
143 <test><!-- TEST 5 --> 143 <test><!-- TEST 5 -->
144 <param name="input_choice" value="2"/> 144 <param name="input_choice" value="2"/>
145 <param name="data" value="feature_table.tsv" ftype="tsv"/> 145 <param name="data" value="feature_table.tsv" ftype="tsv"/>
146 <param name="metadata" value="metadata.tsv" ftype="tsv"/> 146 <param name="metadata" value="metadata.tsv" ftype="tsv"/>
149 <param name="wavelet_length" value="2"/> 149 <param name="wavelet_length" value="2"/>
150 <param name="k" value="20"/> 150 <param name="k" value="20"/>
151 <param name="t" value="0.05"/> 151 <param name="t" value="0.05"/>
152 <param name="t2" value="0.05"/> 152 <param name="t2" value="0.05"/>
153 <param name="alpha" value="0"/> 153 <param name="alpha" value="0"/>
154 <output name="normalized_data" file="normalized_data.tsv"/> 154 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
155 </test> 155 </test>
156 <test><!-- TEST 6 --> 156 <test><!-- TEST 6 -->
157 <param name="input_choice" value="2"/> 157 <param name="input_choice" value="2"/>
158 <param name="data" value="feature_table.parquet" ftype="parquet"/> 158 <param name="data" value="feature_table.parquet" ftype="parquet"/>
159 <param name="metadata" value="metadata.csv" ftype="csv"/> 159 <param name="metadata" value="metadata.csv" ftype="csv"/>
162 <param name="wavelet_length" value="2"/> 162 <param name="wavelet_length" value="2"/>
163 <param name="k" value="20"/> 163 <param name="k" value="20"/>
164 <param name="t" value="0.05"/> 164 <param name="t" value="0.05"/>
165 <param name="t2" value="0.05"/> 165 <param name="t2" value="0.05"/>
166 <param name="alpha" value="0"/> 166 <param name="alpha" value="0"/>
167 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/> 167 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
168 </test> 168 </test>
169 <test><!-- TEST 7 --> 169 <test><!-- TEST 7 -->
170 <param name="input_choice" value="2"/> 170 <param name="input_choice" value="2"/>
171 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/> 171 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
172 <param name="metadata" value="metadata.parquet" ftype="parquet"/> 172 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
176 <param name="wavelet_length" value="2"/> 176 <param name="wavelet_length" value="2"/>
177 <param name="k" value="20"/> 177 <param name="k" value="20"/>
178 <param name="t" value="0.05"/> 178 <param name="t" value="0.05"/>
179 <param name="t2" value="0.05"/> 179 <param name="t2" value="0.05"/>
180 <param name="alpha" value="0"/> 180 <param name="alpha" value="0"/>
181 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/> 181 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
182 </test> 182 </test>
183 <test><!-- TEST 8 --> 183 <test><!-- TEST 8 -->
184 <param name="input_choice" value="2"/> 184 <param name="input_choice" value="2"/>
185 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/> 185 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
186 <param name="metadata" value="metadata.csv" ftype="csv"/> 186 <param name="metadata" value="metadata.csv" ftype="csv"/>
190 <param name="wavelet_length" value="2"/> 190 <param name="wavelet_length" value="2"/>
191 <param name="k" value="20"/> 191 <param name="k" value="20"/>
192 <param name="t" value="0.05"/> 192 <param name="t" value="0.05"/>
193 <param name="t2" value="0.05"/> 193 <param name="t2" value="0.05"/>
194 <param name="alpha" value="0"/> 194 <param name="alpha" value="0"/>
195 <output name="normalized_data" file="normalized_data.csv"/> 195 <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
196 </test> 196 </test>
197 <!-- The following test has different results on three platform I've tried --> 197 <!-- The following test has different results on three platform I've tried -->
198 <!-- <test> 198 <!-- <test>
199 <param name="data" value="input_data_nobatch.csv" ftype="csv"/> 199 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
200 <param name="mode" value="single_batch"/> 200 <param name="mode" value="single_batch"/>