Mercurial > repos > recetox > waveica

annotate waveica.xml @ 1:2bcfd5b450bb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit c52cdb1ab3c4e65ce3b55e29739f16abb8bfd6eb"
author recetox
date Wed, 28 Jul 2021 11:58:20 +0000
parents 2461d20911c9
children d08deef1eb44
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2bcfd5b450bb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit c52cdb1ab3c4e65ce3b55e29739f16abb8bfd6eb"
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1 <tool id="waveica" name="WaveICA" version="0.1.0+galaxy1" python_template_version="3.5">
0
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2
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3 <description>removal of batch effects for untargeted metabolomics data</description>
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4
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5 <requirements>
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6 <container type="docker">recetox/waveica:0.1.0-recetox0</container>
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7 </requirements>
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8
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9 <command detect_errors="aggressive"><![CDATA[
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10 Rscript
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11 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
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12
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13 -e 'normalized_data <- waveica(
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14 data = "$data",
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15 wavelet_filter = "$parameters.wf.wavelet_filter",
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16 wavelet_length = "$parameters.wf.wavelet_length",
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17 k = $parameters.k,
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18 t = $parameters.t,
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19 t2 = $parameters.t2,
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20 alpha = $parameters.alpha,
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21 exclude_blanks = $optional_parameters.exclude_blanks
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22 )'
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23
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24 -e 'store_data(normalized_data,"$normalized_features")'
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25 ]]></command>
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26
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27 <inputs>
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28 <param type="data" name="data" label="Sample-by-matrix data" format="csv" help=""/>
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29 <section name="parameters" title="Normalization Parameters" expanded="True">
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30 <conditional name="wf">
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31 <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="selecting wavelet function and filter length">
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32 <option value="d" selected="True">Daubechies</option>
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33 <option value="la" >Least Asymetric</option>
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34 <option value="bl" >Best Localized</option>
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35 <option value="c" >Coiflet</option>
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36 </param>
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37 <when value="d">
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38 <param name="wavelet_length" type="select" label="filter length">
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39 <option value="2" selected="True">2</option>
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40 <option value="4">4</option>
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41 <option value="6">6</option>
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42 <option value="8">8</option>
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43 <option value="10">10</option>
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44 <option value="12">12</option>
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45 <option value="14">14</option>
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46 <option value="16">16</option>
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47 <option value="18">18</option>
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48 <option value="20">20</option>
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49 </param>
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50 </when>
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51 <when value="la">
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52 <param name="wavelet_length" type="select" label="filter length">
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53 <option value="8">8</option>
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54 <option value="10">10</option>
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55 <option value="12">12</option>
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56 <option value="14">14</option>
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57 <option value="16">16</option>
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58 <option value="18">18</option>
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59 <option value="20">20</option>
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60 </param>
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61 </when>
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62 <when value="bl">
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63 <param name="wavelet_length" type="select" label="filter length">
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64 <option value="14">14</option>
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65 <option value="18">18</option>
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66 <option value="20">20</option>
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67 </param>
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68 </when>
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69 <when value="c">
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70 <param name="wavelet_length" type="select" label="filter length">
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71 <option value="6">6</option>
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72 <option value="12">12</option>
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73 <option value="18">18</option>
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74 <option value="24">24</option>
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75 <option value="30">30</option>
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76 </param>
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77 </when>
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78 </conditional>
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79 <param type="integer" value="20" name="k" label="Number of components to decompose" help="the maximal component that ICA decomposes"/>
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80 <param type="float" value="0.05" name="t" label="Batch-assosiation threshold" help="the threshold to consider a component associate with the batch,
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81 should be between 0 and 1"/>
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82 <param type="float" value="0.05" name="t2" label="Group-assosiation threshold" help="the threshold to consider a component associate with the group,
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83 should be between 0 and 1"/>
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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"/>
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85 </section>
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86 <section name="optional_parameters" expanded="true" title="Optional Parameters">
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87 <param name="exclude_blanks" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
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88 </section>
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89 </inputs>
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90
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91 <outputs>
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92 <data name="normalized_features" format="tsv" />
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93 </outputs>
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94
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95 <tests>
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96 <test>
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97 <param name="data" value="features-test.csv" ftype="csv" />
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98 <param name="wavelet_filter" value="d" />
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99 <param name="filter_length" value="2" />
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100 <param name="k" value="20" />
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101 <param name="t" value="0.05" />
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102 <param name="t2" value="0.05" />
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103 <param name="alpha" value="0" />
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104 <output name="normalized_features" file="features-normalized.tsv" />
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105 </test>
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106 </tests>
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107
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108 <help><![CDATA[
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109 **Description**
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110
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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.
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112
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113 The input is Sample-by-matrix table which must include:
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114
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115 1. Injection order of samples
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116
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117 2. Types of the samples denoted as "blank", "sample" or "QC"
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118
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119 3. Batch numbers
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120
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121 4. Features data
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122
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123 **Documentation**
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124
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125 See original repository for further information: https://github.com/dengkuistat/WaveICA
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126
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127 ]]></help>
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128
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129 <citations>
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130 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
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131 </citations>
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132
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133 </tool>