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comparison waveica.xml @ 0:2461d20911c9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
author recetox
date Thu, 18 Mar 2021 15:53:38 +0000
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-1:000000000000 0:2461d20911c9
1 <tool id="waveica" name="WaveICA" version="0.1.0+galaxy0" python_template_version="3.5">
2
3 <description>removal of batch effects for untargeted metabolomics data</description>
4
5 <requirements>
6 <container type="docker">recetox/waveica:0.1.0-recetox0</container>
7 </requirements>
8
9 <command detect_errors="aggressive"><![CDATA[
10 Rscript
11 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
12
13 -e 'normalized_data <- waveica(
14 data = "$data",
15 wavelet_filter = "$parameters.wf.wavelet_filter",
16 wavelet_length = "$parameters.wf.wavelet_length",
17 k = $parameters.k,
18 t = $parameters.t,
19 t2 = $parameters.t2,
20 alpha = $parameters.alpha,
21 exclude_blanks = $optional_parameters.exclude_blanks
22 )'
23
24 -e 'store_data(normalized_data,"$normalized_features")'
25 ]]></command>
26
27 <inputs>
28 <param type="data" name="data" label="Sample-by-matrix data" format="csv" help=""/>
29 <section name="parameters" title="Normalization Parameters" expanded="True">
30 <conditional name="wf">
31 <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="selecting wavelet function and filter length">
32 <option value="d" selected="True">Daubechies</option>
33 <option value="la" >Least Asymetric</option>
34 <option value="bl" >Best Localized</option>
35 <option value="c" >Coiflet</option>
36 </param>
37 <when value="d">
38 <param name="wavelet_length" type="select" label="filter length">
39 <option value="2" selected="True">2</option>
40 <option value="4">4</option>
41 <option value="6">6</option>
42 <option value="8">8</option>
43 <option value="10">10</option>
44 <option value="12">12</option>
45 <option value="14">14</option>
46 <option value="16">16</option>
47 <option value="18">18</option>
48 <option value="20">20</option>
49 </param>
50 </when>
51 <when value="la">
52 <param name="wavelet_length" type="select" label="filter length">
53 <option value="8">8</option>
54 <option value="10">10</option>
55 <option value="12">12</option>
56 <option value="14">14</option>
57 <option value="16">16</option>
58 <option value="18">18</option>
59 <option value="20">20</option>
60 </param>
61 </when>
62 <when value="bl">
63 <param name="wavelet_length" type="select" label="filter length">
64 <option value="14">14</option>
65 <option value="18">18</option>
66 <option value="20">20</option>
67 </param>
68 </when>
69 <when value="c">
70 <param name="wavelet_length" type="select" label="filter length">
71 <option value="6">6</option>
72 <option value="12">12</option>
73 <option value="18">18</option>
74 <option value="24">24</option>
75 <option value="30">30</option>
76 </param>
77 </when>
78 </conditional>
79 <param type="integer" value="20" name="k" label="Number of components to decompose" help="the maximal component that ICA decomposes"/>
80 <param type="float" value="0.05" name="t" label="Batch-assosiation threshold" help="the threshold to consider a component associate with the batch,
81 should be between 0 and 1"/>
82 <param type="float" value="0.05" name="t2" label="Group-assosiation threshold" help="the threshold to consider a component associate with the group,
83 should be between 0 and 1"/>
84 <param type="float" value="0" name="alpha" label="Alpha" help="the trade-off value between the independence of samples and those of variables and should be between 0 and 1"/>
85 </section>
86 <section name="optional_parameters" expanded="true" title="Optional Parameters">
87 <param name="exclude_blanks" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
88 </section>
89 </inputs>
90
91 <outputs>
92 <data name="normalized_features" format="tsv" />
93 </outputs>
94
95 <tests>
96 <test>
97 <param name="data" value="features-test.csv" ftype="csv" />
98 <param name="wavelet_filter" value="d" />
99 <param name="filter_length" value="2" />
100 <param name="k" value="20" />
101 <param name="t" value="0.05" />
102 <param name="t2" value="0.05" />
103 <param name="alpha" value="0" />
104 <output name="normalized_features" file="features-normalized.tsv" />
105 </test>
106 </tests>
107
108 <help><![CDATA[
109 **Description**
110
111 Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. The WaveICA R package provides a new algorithm to removing batch effects for metabolomics data.
112
113 The input is Sample-by-matrix table which must include:
114
115 1. Injection order of samples
116
117 2. Types of the samples denoted as "blank", "sample" or "QC"
118
119 3. Batch numbers
120
121 4. Features data
122
123 **Documentation**
124
125 See original repository for further information: https://github.com/dengkuistat/WaveICA
126
127 ]]></help>
128
129 <citations>
130 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
131 </citations>
132
133 </tool>