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comparison waveica.xml @ 7:385b1221be44 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
author recetox
date Fri, 23 Jun 2023 07:27:12 +0000
parents cf3f2f964d80
children
comparison
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6:cf3f2f964d80 7:385b1221be44
1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy2" python_template_version="3.5"> 1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy3" python_template_version="3.5">
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="creator"/> 7 <expand macro="creator"/>
7 8
8 <requirements> 9 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
10 <requirement type="package" version="8.0.0">r-arrow</requirement> 11 <requirement type="package" version="8.0.0">r-arrow</requirement>
17 -e 'normalized_data <- waveica( 18 -e 'normalized_data <- waveica(
18 file = "$input_num.data", 19 file = "$input_num.data",
19 #if $input_num.input_choice == "2": 20 #if $input_num.input_choice == "2":
20 metadata = "$input_num.input_metadata.metadata", 21 metadata = "$input_num.input_metadata.metadata",
21 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", 22 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
23 transpose = $input_num.transpose_feature_table,
22 #else: 24 #else:
23 ext = "$input_num.data.ext", 25 ext = "$input_num.data.ext",
24 #end if 26 #end if
25 wavelet_filter = "$wf.wavelet_filter", 27 wavelet_filter = "$wf.wavelet_filter",
26 wavelet_length = "$wf.wavelet_length", 28 wavelet_length = "$wf.wavelet_length",
34 -e 'normalized_data <- waveica_singlebatch( 36 -e 'normalized_data <- waveica_singlebatch(
35 file = "$input_num.data", 37 file = "$input_num.data",
36 #if $input_num.input_choice == "2": 38 #if $input_num.input_choice == "2":
37 metadata = "$input_num.input_metadata.metadata", 39 metadata = "$input_num.input_metadata.metadata",
38 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", 40 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
41 transpose = $input_num.transpose_feature_table,
39 #else: 42 #else:
40 ext = "$input_num.data.ext", 43 ext = "$input_num.data.ext",
41 #end if 44 #end if
42 wavelet_filter = "$wf.wavelet_filter", 45 wavelet_filter = "$wf.wavelet_filter",
43 wavelet_length = "$wf.wavelet_length", 46 wavelet_length = "$wf.wavelet_length",
59 </param> 62 </param>
60 <when value="1"> 63 <when value="1">
61 <expand macro="input_data"/> 64 <expand macro="input_data"/>
62 </when> 65 </when>
63 <when value="2"> 66 <when value="2">
67 <expand macro="input_data"/>
64 <section name="input_metadata" title="Input metadata table" expanded="true"> 68 <section name="input_metadata" title="Input metadata table" expanded="true">
65 <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" /> 69 <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" />
66 </section> 70 </section>
67 <expand macro="input_data"/> 71 <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
72 truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
68 </when> 73 </when>
69 </conditional> 74 </conditional>
70 <expand macro="general_parameters"/> 75 <expand macro="general_parameters"/>
71 <expand macro="wf"/> 76 <expand macro="wf"/>
72 <conditional name="batch_correction"> 77 <conditional name="batch_correction">
91 <tests> 96 <tests>
92 <test><!-- TEST 1 --> 97 <test><!-- TEST 1 -->
93 <param name="data" value="input_data.csv" ftype="csv"/> 98 <param name="data" value="input_data.csv" ftype="csv"/>
94 <param name="mode" value="batchwise"/> 99 <param name="mode" value="batchwise"/>
95 <param name="wavelet_filter" value="d"/> 100 <param name="wavelet_filter" value="d"/>
96 <param name="filter_length" value="2"/> 101 <param name="wavelet_length" value="2"/>
97 <param name="k" value="20"/> 102 <param name="k" value="20"/>
98 <param name="t" value="0.05"/> 103 <param name="t" value="0.05"/>
99 <param name="t2" value="0.05"/> 104 <param name="t2" value="0.05"/>
100 <param name="alpha" value="0"/> 105 <param name="alpha" value="0"/>
101 <output name="normalized_data" file="normalized_data.csv"/> 106 <output name="normalized_data" file="normalized_data.csv"/>
102 </test> 107 </test>
103 <test><!-- TEST 2 --> 108 <test><!-- TEST 2 -->
104 <param name="data" value="input_data.tsv" ftype="tsv"/> 109 <param name="data" value="input_data.tsv" ftype="tsv"/>
105 <param name="mode" value="batchwise"/> 110 <param name="mode" value="batchwise"/>
106 <param name="wavelet_filter" value="d"/> 111 <param name="wavelet_filter" value="d"/>
107 <param name="filter_length" value="2"/> 112 <param name="wavelet_length" value="2"/>
108 <param name="k" value="20"/> 113 <param name="k" value="20"/>
109 <param name="t" value="0.05"/> 114 <param name="t" value="0.05"/>
110 <param name="t2" value="0.05"/> 115 <param name="t2" value="0.05"/>
111 <param name="alpha" value="0"/> 116 <param name="alpha" value="0"/>
112 <output name="normalized_data" file="normalized_data.tsv"/> 117 <output name="normalized_data" file="normalized_data.tsv"/>
113 </test> 118 </test>
114 <test><!-- TEST 3 --> 119 <test><!-- TEST 3 -->
115 <param name="data" value="input_data.parquet" ftype="parquet"/> 120 <param name="data" value="input_data.parquet" ftype="parquet"/>
116 <param name="mode" value="batchwise"/> 121 <param name="mode" value="batchwise"/>
117 <param name="wavelet_filter" value="d"/> 122 <param name="wavelet_filter" value="d"/>
118 <param name="filter_length" value="2"/> 123 <param name="wavelet_length" value="2"/>
119 <param name="k" value="20"/> 124 <param name="k" value="20"/>
120 <param name="t" value="0.05"/> 125 <param name="t" value="0.05"/>
121 <param name="t2" value="0.05"/> 126 <param name="t2" value="0.05"/>
122 <param name="alpha" value="0"/> 127 <param name="alpha" value="0"/>
123 <output name="normalized_data" file="normalized_data.parquet"/> 128 <output name="normalized_data" file="normalized_data.parquet"/>
126 <param name="input_choice" value="2"/> 131 <param name="input_choice" value="2"/>
127 <param name="data" value="feature_table.csv" ftype="csv"/> 132 <param name="data" value="feature_table.csv" ftype="csv"/>
128 <param name="metadata" value="metadata.csv" ftype="csv"/> 133 <param name="metadata" value="metadata.csv" ftype="csv"/>
129 <param name="mode" value="batchwise"/> 134 <param name="mode" value="batchwise"/>
130 <param name="wavelet_filter" value="d"/> 135 <param name="wavelet_filter" value="d"/>
131 <param name="filter_length" value="2"/> 136 <param name="wavelet_length" value="2"/>
132 <param name="k" value="20"/> 137 <param name="k" value="20"/>
133 <param name="t" value="0.05"/> 138 <param name="t" value="0.05"/>
134 <param name="t2" value="0.05"/> 139 <param name="t2" value="0.05"/>
135 <param name="alpha" value="0"/> 140 <param name="alpha" value="0"/>
136 <output name="normalized_data" file="normalized_data.csv"/> 141 <output name="normalized_data" file="normalized_data.csv"/>
139 <param name="input_choice" value="2"/> 144 <param name="input_choice" value="2"/>
140 <param name="data" value="feature_table.tsv" ftype="tsv"/> 145 <param name="data" value="feature_table.tsv" ftype="tsv"/>
141 <param name="metadata" value="metadata.tsv" ftype="tsv"/> 146 <param name="metadata" value="metadata.tsv" ftype="tsv"/>
142 <param name="mode" value="batchwise"/> 147 <param name="mode" value="batchwise"/>
143 <param name="wavelet_filter" value="d"/> 148 <param name="wavelet_filter" value="d"/>
144 <param name="filter_length" value="2"/> 149 <param name="wavelet_length" value="2"/>
145 <param name="k" value="20"/> 150 <param name="k" value="20"/>
146 <param name="t" value="0.05"/> 151 <param name="t" value="0.05"/>
147 <param name="t2" value="0.05"/> 152 <param name="t2" value="0.05"/>
148 <param name="alpha" value="0"/> 153 <param name="alpha" value="0"/>
149 <output name="normalized_data" file="normalized_data.tsv"/> 154 <output name="normalized_data" file="normalized_data.tsv"/>
152 <param name="input_choice" value="2"/> 157 <param name="input_choice" value="2"/>
153 <param name="data" value="feature_table.parquet" ftype="parquet"/> 158 <param name="data" value="feature_table.parquet" ftype="parquet"/>
154 <param name="metadata" value="metadata.csv" ftype="csv"/> 159 <param name="metadata" value="metadata.csv" ftype="csv"/>
155 <param name="mode" value="batchwise"/> 160 <param name="mode" value="batchwise"/>
156 <param name="wavelet_filter" value="d"/> 161 <param name="wavelet_filter" value="d"/>
157 <param name="filter_length" value="2"/> 162 <param name="wavelet_length" value="2"/>
158 <param name="k" value="20"/> 163 <param name="k" value="20"/>
159 <param name="t" value="0.05"/> 164 <param name="t" value="0.05"/>
160 <param name="t2" value="0.05"/> 165 <param name="t2" value="0.05"/>
161 <param name="alpha" value="0"/> 166 <param name="alpha" value="0"/>
162 <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"/>
168 </test>
169 <test><!-- TEST 7 -->
170 <param name="input_choice" value="2"/>
171 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
172 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
173 <param name="transpose_feature_table" value="TRUE"/>
174 <param name="mode" value="batchwise"/>
175 <param name="wavelet_filter" value="d"/>
176 <param name="wavelet_length" value="2"/>
177 <param name="k" value="20"/>
178 <param name="t" value="0.05"/>
179 <param name="t2" value="0.05"/>
180 <param name="alpha" value="0"/>
181 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
182 </test>
183 <test><!-- TEST 8 -->
184 <param name="input_choice" value="2"/>
185 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
186 <param name="metadata" value="metadata.csv" ftype="csv"/>
187 <param name="transpose_feature_table" value="TRUE"/>
188 <param name="mode" value="batchwise"/>
189 <param name="wavelet_filter" value="d"/>
190 <param name="wavelet_length" value="2"/>
191 <param name="k" value="20"/>
192 <param name="t" value="0.05"/>
193 <param name="t2" value="0.05"/>
194 <param name="alpha" value="0"/>
195 <output name="normalized_data" file="normalized_data.csv"/>
163 </test> 196 </test>
164 <!-- 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 -->
165 <!-- <test> 198 <!-- <test>
166 <param name="data" value="input_data_nobatch.csv" ftype="csv"/> 199 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
167 <param name="mode" value="single_batch"/> 200 <param name="mode" value="single_batch"/>