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comparison waveica.xml @ 0:328710890963 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
author recetox
date Wed, 23 Mar 2022 11:35:30 +0000
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children b77023c41c76
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-1:000000000000 0:328710890963
1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy1" python_template_version="3.5">
2 <description>removal of batch effects for untargeted metabolomics data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator"/>
7
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
10 </requirements>
11 <command detect_errors="aggressive"><![CDATA[
12 Rscript
13 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
14
15 #if $batch_correction.mode == "batchwise":
16 -e 'normalized_data <- waveica(
17 data = "$data",
18 wavelet_filter = "$wf.wavelet_filter",
19 wavelet_length = "$wf.wavelet_length",
20 k = $k,
21 t = $batch_correction.t,
22 t2 = $batch_correction.t2,
23 alpha = $alpha,
24 exclude_blanks = $exclude_blanks
25 )'
26 #else if $batch_correction.mode == "single_batch":
27 -e 'normalized_data <- waveica_singlebatch(
28 data = "$data",
29 wavelet_filter = "$wf.wavelet_filter",
30 wavelet_length = "$wf.wavelet_length",
31 k = $k,
32 alpha = $alpha,
33 cutoff = $batch_correction.cutoff,
34 exclude_blanks = $exclude_blanks
35 )'
36 #end if
37
38 -e 'store_data(normalized_data,"$normalized_data")'
39 ]]></command>
40
41 <inputs>
42 <expand macro="general_parameters"/>
43 <expand macro="wf"/>
44 <conditional name="batch_correction">
45 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
46 inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
47 requires no batch information [2]">
48 <option value="batchwise" selected="true">Multiple batches</option>
49 <option value="single_batch">Single batch (or no batch information)</option>
50 </param>
51 <when value="batchwise">
52 <expand macro="batchwise_parameters"/>
53 </when>
54 <when value="single_batch">
55 <expand macro="singlebatch_parameters"/>
56 </when>
57 </conditional>
58 <expand macro="exclude_blanks"/>
59 </inputs>
60
61 <expand macro="outputs"/>
62
63 <tests>
64 <test>
65 <param name="data" value="input_data.csv" ftype="csv"/>
66 <param name="mode" value="batchwise"/>
67 <param name="wavelet_filter" value="d"/>
68 <param name="filter_length" value="2"/>
69 <param name="k" value="20"/>
70 <param name="t" value="0.05"/>
71 <param name="t2" value="0.05"/>
72 <param name="alpha" value="0"/>
73 <output name="normalized_data" file="normalized_data.tsv"/>
74 </test>
75 <!-- The following test has different results on three platform I've tried -->
76 <!-- <test>
77 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
78 <param name="mode" value="single_batch"/>
79 <param name="wavelet_filter" value="d"/>
80 <param name="filter_length" value="2"/>
81 <param name="k" value="20"/>
82 <param name="alpha" value="0"/>
83 <param name="cutoff" value="0"/>
84 <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
85 </test> -->
86 <test expect_failure="true">
87 <param name="data" value="na_data.csv" ftype="csv"/>
88 </test>
89 <test expect_failure="true">
90 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
91 </test>
92 </tests>
93
94 <help>
95 <![CDATA[
96 @HELP@
97 ]]>
98 </help>
99
100 <citations>
101 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
102 <citation type="doi">10.1007/s11306-021-01839-7</citation>
103 </citations>
104
105 </tool>