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annotate waveica.xml @ 5:fba892edb9d9 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 11:35:00 +0000
parents 8b55efc7d117
children cf3f2f964d80
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1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy1" python_template_version="3.5">
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2 <description>removal of batch effects for untargeted metabolomics data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
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6 <expand macro="creator"/>
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7
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
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10 </requirements>
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11 <command detect_errors="aggressive"><![CDATA[
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12 Rscript
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13 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
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14
4
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15 #if $batch_correction.mode == "batchwise":
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16 -e 'normalized_data <- waveica(
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17 data = "$data",
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18 wavelet_filter = "$wf.wavelet_filter",
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19 wavelet_length = "$wf.wavelet_length",
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20 k = $k,
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21 t = $batch_correction.t,
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22 t2 = $batch_correction.t2,
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23 alpha = $alpha,
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24 exclude_blanks = $exclude_blanks
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25 )'
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26 #else if $batch_correction.mode == "single_batch":
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27 -e 'normalized_data <- waveica_singlebatch(
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28 data = "$data",
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29 wavelet_filter = "$wf.wavelet_filter",
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30 wavelet_length = "$wf.wavelet_length",
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31 k = $k,
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32 alpha = $alpha,
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33 cutoff = $batch_correction.cutoff,
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34 exclude_blanks = $exclude_blanks
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35 )'
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36 #end if
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37
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38 -e 'store_data(normalized_data,"$normalized_data")'
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39 ]]></command>
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41 <inputs>
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42 <expand macro="general_parameters"/>
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43 <expand macro="wf"/>
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44 <conditional name="batch_correction">
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45 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
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46 inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
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47 requires no batch information [2]">
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48 <option value="batchwise" selected="true">Multiple batches</option>
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49 <option value="single_batch">Single batch (or no batch information)</option>
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50 </param>
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51 <when value="batchwise">
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52 <expand macro="batchwise_parameters"/>
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53 </when>
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54 <when value="single_batch">
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55 <expand macro="singlebatch_parameters"/>
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56 </when>
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57 </conditional>
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58 <expand macro="exclude_blanks"/>
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59 </inputs>
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60
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61 <expand macro="outputs"/>
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62
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63 <tests>
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64 <test>
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65 <param name="data" value="input_data.csv" ftype="csv"/>
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66 <param name="mode" value="batchwise"/>
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67 <param name="wavelet_filter" value="d"/>
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68 <param name="filter_length" value="2"/>
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69 <param name="k" value="20"/>
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70 <param name="t" value="0.05"/>
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71 <param name="t2" value="0.05"/>
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72 <param name="alpha" value="0"/>
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73 <output name="normalized_data" file="normalized_data.tsv"/>
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74 </test>
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75 <!-- The following test has different results on three platform I've tried -->
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76 <!-- <test>
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77 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
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78 <param name="mode" value="single_batch"/>
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79 <param name="wavelet_filter" value="d"/>
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80 <param name="filter_length" value="2"/>
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81 <param name="k" value="20"/>
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82 <param name="alpha" value="0"/>
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83 <param name="cutoff" value="0"/>
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84 <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
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85 </test> -->
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86 <test expect_failure="true">
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87 <param name="data" value="na_data.csv" ftype="csv"/>
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88 </test>
2
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89 <test expect_failure="true">
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90 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
0
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91 </test>
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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92 </tests>
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93
5
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94 <help>
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95 <![CDATA[
fba892edb9d9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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96 @HELP@
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97 ]]>
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98 </help>
0
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99
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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100 <citations>
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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101 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
4
8b55efc7d117 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit aa8206a01efc1813f2586584782f28a73a17fe86"
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102 <citation type="doi">10.1007/s11306-021-01839-7</citation>
0
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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103 </citations>
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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104
5
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105 </tool>