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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 013d7c85fa9d77b8a27d194b350cd6b2d127a80f
author recetox
date Thu, 06 Jun 2024 12:25:05 +0000
parents e424fa636281
children
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7
1a2aeb8137bf planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 013d7c85fa9d77b8a27d194b350cd6b2d127a80f
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1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy7" profile="21.09">
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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>
2
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6 <expand macro="annotation"/>
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7 <expand macro="creator"/>
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8
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
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11 <requirement type="package" version="8.0.0">r-arrow</requirement>
0
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12 </requirements>
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13 <command detect_errors="aggressive"><![CDATA[
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14 Rscript
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15 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
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16
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17 #if $batch_correction.mode == "batchwise":
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18 -e 'normalized_data <- waveica(
1
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19 file = "$input_num.data",
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20 #if $input_num.input_choice == "2":
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21 metadata = "$input_num.input_metadata.metadata",
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22 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
2
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23 transpose = $input_num.transpose_feature_table,
1
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24 #else:
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25 ext = "$input_num.data.ext",
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26 #end if
0
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27 wavelet_filter = "$wf.wavelet_filter",
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28 wavelet_length = "$wf.wavelet_length",
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29 k = $k,
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30 t = $batch_correction.t,
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31 t2 = $batch_correction.t2,
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32 alpha = $alpha,
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33 exclude_blanks = $exclude_blanks
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34 )'
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35 #else if $batch_correction.mode == "single_batch":
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36 -e 'normalized_data <- waveica_singlebatch(
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37 file = "$input_num.data",
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38 #if $input_num.input_choice == "2":
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39 metadata = "$input_num.input_metadata.metadata",
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40 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
2
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41 transpose = $input_num.transpose_feature_table,
1
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42 #else:
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43 ext = "$input_num.data.ext",
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44 #end if
0
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45 wavelet_filter = "$wf.wavelet_filter",
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46 wavelet_length = "$wf.wavelet_length",
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47 k = $k,
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48 alpha = $alpha,
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49 cutoff = $batch_correction.cutoff,
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50 exclude_blanks = $exclude_blanks
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51 )'
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52 #end if
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53
7
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54 -e 'store_data(normalized_data, "$normalized_data", "$metadata", "$input_num.data.ext", $keep_two_output)'
0
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55 ]]></command>
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56
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57 <inputs>
1
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58 <conditional name="input_num">
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59 <param name="input_choice" type="select" label="Choose input files:">
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60 <option value="1" selected="true">1: intensity-by-feature table with metadata</option>
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61 <option value="2">2: intensity-by-feature table and metadata table separately</option>
1
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62 </param>
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63 <when value="1">
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64 <expand macro="input_data"/>
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65 </when>
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66 <when value="2">
2
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67 <expand macro="input_data"/>
1
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68 <section name="input_metadata" title="Input metadata table" expanded="true">
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69 <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" />
2
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70 </section>
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71 <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
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72 truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
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73 </when>
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74 </conditional>
0
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75 <expand macro="general_parameters"/>
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76 <expand macro="wf"/>
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77 <conditional name="batch_correction">
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78 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
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79 inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
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80 requires no batch information [2]">
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81 <option value="batchwise" selected="true">Multiple batches</option>
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82 <option value="single_batch">Single batch (or no batch information)</option>
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83 </param>
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84 <when value="batchwise">
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85 <expand macro="batchwise_parameters"/>
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86 </when>
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87 <when value="single_batch">
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88 <expand macro="singlebatch_parameters"/>
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89 </when>
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90 </conditional>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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91 <expand macro="exclude_blanks"/>
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92 <expand macro="split_output"/>
0
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93 </inputs>
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94
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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95 <expand macro="outputs"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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96
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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97 <tests>
7
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98 <test expect_num_outputs="1"><!-- TEST 1 -->
0
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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99 <param name="data" value="input_data.csv" ftype="csv"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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100 <param name="mode" value="batchwise"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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101 <param name="wavelet_filter" value="d"/>
2
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102 <param name="wavelet_length" value="2"/>
0
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103 <param name="k" value="20"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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104 <param name="t" value="0.05"/>
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105 <param name="t2" value="0.05"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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106 <param name="alpha" value="0"/>
7
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107 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
1
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108 </test>
7
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109 <test expect_num_outputs="1"><!-- TEST 2 -->
1
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110 <param name="data" value="input_data.tsv" ftype="tsv"/>
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111 <param name="mode" value="batchwise"/>
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112 <param name="wavelet_filter" value="d"/>
2
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113 <param name="wavelet_length" value="2"/>
1
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114 <param name="k" value="20"/>
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115 <param name="t" value="0.05"/>
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116 <param name="t2" value="0.05"/>
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117 <param name="alpha" value="0"/>
7
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118 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
0
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119 </test>
7
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120 <test expect_num_outputs="1"><!-- TEST 3 -->
1
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121 <param name="data" value="input_data.parquet" ftype="parquet"/>
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122 <param name="mode" value="batchwise"/>
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123 <param name="wavelet_filter" value="d"/>
2
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124 <param name="wavelet_length" value="2"/>
1
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125 <param name="k" value="20"/>
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126 <param name="t" value="0.05"/>
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127 <param name="t2" value="0.05"/>
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128 <param name="alpha" value="0"/>
4
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129 <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
1
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130 </test>
7
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131 <test expect_num_outputs="1"><!-- TEST 4 -->
1
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132 <param name="input_choice" value="2"/>
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133 <param name="data" value="feature_table.csv" ftype="csv"/>
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134 <param name="metadata" value="metadata.csv" ftype="csv"/>
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135 <param name="mode" value="batchwise"/>
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136 <param name="wavelet_filter" value="d"/>
2
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137 <param name="wavelet_length" value="2"/>
1
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138 <param name="k" value="20"/>
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139 <param name="t" value="0.05"/>
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140 <param name="t2" value="0.05"/>
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141 <param name="alpha" value="0"/>
7
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142 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
1
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143 </test>
7
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144 <test expect_num_outputs="1"><!-- TEST 5 -->
1
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145 <param name="input_choice" value="2"/>
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146 <param name="data" value="feature_table.tsv" ftype="tsv"/>
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147 <param name="metadata" value="metadata.tsv" ftype="tsv"/>
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148 <param name="mode" value="batchwise"/>
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149 <param name="wavelet_filter" value="d"/>
2
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150 <param name="wavelet_length" value="2"/>
1
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151 <param name="k" value="20"/>
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152 <param name="t" value="0.05"/>
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153 <param name="t2" value="0.05"/>
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154 <param name="alpha" value="0"/>
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155 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
1
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156 </test>
7
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157 <test expect_num_outputs="1"><!-- TEST 6 -->
1
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158 <param name="input_choice" value="2"/>
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159 <param name="data" value="feature_table.parquet" ftype="parquet"/>
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160 <param name="metadata" value="metadata.csv" ftype="csv"/>
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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161 <param name="mode" value="batchwise"/>
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162 <param name="wavelet_filter" value="d"/>
2
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163 <param name="wavelet_length" value="2"/>
1
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164 <param name="k" value="20"/>
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165 <param name="t" value="0.05"/>
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166 <param name="t2" value="0.05"/>
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167 <param name="alpha" value="0"/>
4
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168 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
1
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169 </test>
7
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170 <test expect_num_outputs="1"><!-- TEST 7 -->
2
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171 <param name="input_choice" value="2"/>
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172 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
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173 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
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174 <param name="transpose_feature_table" value="TRUE"/>
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175 <param name="mode" value="batchwise"/>
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176 <param name="wavelet_filter" value="d"/>
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177 <param name="wavelet_length" value="2"/>
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178 <param name="k" value="20"/>
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179 <param name="t" value="0.05"/>
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180 <param name="t2" value="0.05"/>
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181 <param name="alpha" value="0"/>
4
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182 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
2
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183 </test>
7
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184 <test expect_num_outputs="1"><!-- TEST 8 -->
2
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185 <param name="input_choice" value="2"/>
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186 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
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187 <param name="metadata" value="metadata.csv" ftype="csv"/>
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188 <param name="transpose_feature_table" value="TRUE"/>
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189 <param name="mode" value="batchwise"/>
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190 <param name="wavelet_filter" value="d"/>
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191 <param name="wavelet_length" value="2"/>
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192 <param name="k" value="20"/>
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193 <param name="t" value="0.05"/>
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194 <param name="t2" value="0.05"/>
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195 <param name="alpha" value="0"/>
7
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196 <output name="normalized_data" file="normalized_data.tsv" ftype="tabular"/>
2
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197 </test>
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198 <!-- The following test has different results on three platform I've tried -->
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199 <!-- <test>
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200 <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
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201 <param name="mode" value="single_batch"/>
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202 <param name="wavelet_filter" value="d"/>
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203 <param name="filter_length" value="2"/>
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204 <param name="k" value="20"/>
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205 <param name="alpha" value="0"/>
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206 <param name="cutoff" value="0"/>
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207 <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
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208 </test> -->
7
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209 <test expect_num_outputs="2"><!-- TEST 9 -->
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210 <param name="input_choice" value="2"/>
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211 <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
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212 <param name="metadata" value="metadata.parquet" ftype="parquet"/>
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213 <param name="transpose_feature_table" value="TRUE"/>
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214 <param name="mode" value="batchwise"/>
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215 <param name="wavelet_filter" value="d"/>
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216 <param name="wavelet_length" value="2"/>
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217 <param name="k" value="20"/>
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218 <param name="t" value="0.05"/>
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219 <param name="t2" value="0.05"/>
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220 <param name="alpha" value="0"/>
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221 <param name="keep_two_output" value="TRUE"/>
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222 <output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
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223 <output name="metadata" file="test9_output2.parquet" ftype="parquet"/>
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224 </test>
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225 <test expect_num_outputs="2"><!-- TEST 10 -->
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226 <param name="input_choice" value="2"/>
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227 <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
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228 <param name="metadata" value="metadata.csv" ftype="csv"/>
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229 <param name="transpose_feature_table" value="TRUE"/>
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230 <param name="mode" value="batchwise"/>
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231 <param name="wavelet_filter" value="d"/>
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232 <param name="wavelet_length" value="2"/>
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233 <param name="k" value="20"/>
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234 <param name="t" value="0.05"/>
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235 <param name="t2" value="0.05"/>
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236 <param name="alpha" value="0"/>
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237 <param name="keep_two_output" value="TRUE"/>
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238 <output name="normalized_data" file="test10_output1.tsv" ftype="tabular"/>
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239 <output name="metadata" file="test10_output2.tsv" ftype="tabular"/>
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240 </test>
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241 <test expect_failure="true"><!-- TEST 11 -->
0
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242 <param name="data" value="na_data.csv" ftype="csv"/>
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243 </test>
7
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244 <test expect_failure="true"><!-- TEST 12 -->
0
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245 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
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246 </test>
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247 </tests>
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248
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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249 <help>
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250 <![CDATA[
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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251 @HELP@
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252 ]]>
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253 </help>
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254
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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255 <citations>
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256 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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257 <citation type="doi">10.1007/s11306-021-01839-7</citation>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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258 </citations>
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259
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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260 </tool>