Mercurial > repos > recetox > waveica
annotate waveica.xml @ 1:b77023c41c76 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
author | recetox |
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date | Thu, 29 Sep 2022 15:21:04 +0000 |
parents | 328710890963 |
children | 6480c6d5fa36 |
rev | line source |
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1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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1 <tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy2" python_template_version="3.5"> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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2 <description>removal of batch effects for untargeted metabolomics data</description> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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3 <macros> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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4 <import>macros.xml</import> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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5 </macros> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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6 <expand macro="creator"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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7 |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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8 <requirements> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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9 <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement> |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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10 <requirement type="package" version="8.0.0">r-arrow</requirement> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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11 </requirements> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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12 <command detect_errors="aggressive"><![CDATA[ |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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13 Rscript |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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14 -e 'source("${__tool_directory__}/waveica_wrapper.R")' |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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15 |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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16 #if $batch_correction.mode == "batchwise": |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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17 -e 'normalized_data <- waveica( |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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18 file = "$input_num.data", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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19 #if $input_num.input_choice == "2": |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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20 metadata = "$input_num.input_metadata.metadata", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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21 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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22 #else: |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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23 ext = "$input_num.data.ext", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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24 #end if |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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25 wavelet_filter = "$wf.wavelet_filter", |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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26 wavelet_length = "$wf.wavelet_length", |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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27 k = $k, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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28 t = $batch_correction.t, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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29 t2 = $batch_correction.t2, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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30 alpha = $alpha, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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31 exclude_blanks = $exclude_blanks |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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32 )' |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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33 #else if $batch_correction.mode == "single_batch": |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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34 -e 'normalized_data <- waveica_singlebatch( |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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35 file = "$input_num.data", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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36 #if $input_num.input_choice == "2": |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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37 metadata = "$input_num.input_metadata.metadata", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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38 ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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39 #else: |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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40 ext = "$input_num.data.ext", |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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41 #end if |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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42 wavelet_filter = "$wf.wavelet_filter", |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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43 wavelet_length = "$wf.wavelet_length", |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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44 k = $k, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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45 alpha = $alpha, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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46 cutoff = $batch_correction.cutoff, |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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47 exclude_blanks = $exclude_blanks |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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48 )' |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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49 #end if |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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50 |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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51 -e 'store_data(normalized_data, "$normalized_data", "$input_num.data.ext")' |
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328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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52 ]]></command> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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53 |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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54 <inputs> |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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55 <conditional name="input_num"> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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56 <param name="input_choice" type="select" label="Choose input files:"> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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57 <option value="1" selected="true">1</option> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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58 <option value="2">2</option> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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59 </param> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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60 <when value="1"> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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61 <expand macro="input_data"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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62 </when> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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63 <when value="2"> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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64 <section name="input_metadata" title="Input metadata table" expanded="true"> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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65 <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" /> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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66 </section> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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67 <expand macro="input_data"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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68 </when> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
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69 </conditional> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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70 <expand macro="general_parameters"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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71 <expand macro="wf"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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72 <conditional name="batch_correction"> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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73 <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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74 inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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75 requires no batch information [2]"> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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76 <option value="batchwise" selected="true">Multiple batches</option> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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77 <option value="single_batch">Single batch (or no batch information)</option> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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78 </param> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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79 <when value="batchwise"> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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80 <expand macro="batchwise_parameters"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
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81 </when> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
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82 <when value="single_batch"> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
83 <expand macro="singlebatch_parameters"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
84 </when> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
85 </conditional> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
86 <expand macro="exclude_blanks"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
87 </inputs> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
88 |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
89 <expand macro="outputs"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
90 |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
91 <tests> |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
92 <test><!-- TEST 1 --> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
93 <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"
recetox
parents:
diff
changeset
|
94 <param name="mode" value="batchwise"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
95 <param name="wavelet_filter" value="d"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
96 <param name="filter_length" value="2"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
97 <param name="k" value="20"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
98 <param name="t" value="0.05"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
99 <param name="t2" value="0.05"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
100 <param name="alpha" value="0"/> |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
101 <output name="normalized_data" file="normalized_data.csv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
102 </test> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
103 <test><!-- TEST 2 --> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
104 <param name="data" value="input_data.tsv" ftype="tsv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
105 <param name="mode" value="batchwise"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
106 <param name="wavelet_filter" value="d"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
107 <param name="filter_length" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
108 <param name="k" value="20"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
109 <param name="t" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
110 <param name="t2" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
111 <param name="alpha" value="0"/> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
112 <output name="normalized_data" file="normalized_data.tsv"/> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
113 </test> |
1
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
114 <test><!-- TEST 3 --> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
115 <param name="data" value="input_data.parquet" ftype="parquet"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
116 <param name="mode" value="batchwise"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
117 <param name="wavelet_filter" value="d"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
118 <param name="filter_length" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
119 <param name="k" value="20"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
120 <param name="t" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
121 <param name="t2" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
122 <param name="alpha" value="0"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
123 <output name="normalized_data" file="normalized_data.parquet"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
124 </test> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
125 <test><!-- TEST 4 --> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
126 <param name="input_choice" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
127 <param name="data" value="feature_table.csv" ftype="csv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
128 <param name="metadata" value="metadata.csv" ftype="csv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
129 <param name="mode" value="batchwise"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
130 <param name="wavelet_filter" value="d"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
131 <param name="filter_length" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
132 <param name="k" value="20"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
133 <param name="t" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
134 <param name="t2" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
135 <param name="alpha" value="0"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
136 <output name="normalized_data" file="normalized_data.csv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
137 </test> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
138 <test><!-- TEST 5 --> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
139 <param name="input_choice" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
140 <param name="data" value="feature_table.tsv" ftype="tsv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
141 <param name="metadata" value="metadata.tsv" ftype="tsv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
142 <param name="mode" value="batchwise"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
143 <param name="wavelet_filter" value="d"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
144 <param name="filter_length" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
145 <param name="k" value="20"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
146 <param name="t" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
147 <param name="t2" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
148 <param name="alpha" value="0"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
149 <output name="normalized_data" file="normalized_data.tsv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
150 </test> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
151 <test><!-- TEST 6 --> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
152 <param name="input_choice" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
153 <param name="data" value="feature_table.parquet" ftype="parquet"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
154 <param name="metadata" value="metadata.csv" ftype="csv"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
155 <param name="mode" value="batchwise"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
156 <param name="wavelet_filter" value="d"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
157 <param name="filter_length" value="2"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
158 <param name="k" value="20"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
159 <param name="t" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
160 <param name="t2" value="0.05"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
161 <param name="alpha" value="0"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
162 <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/> |
b77023c41c76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
recetox
parents:
0
diff
changeset
|
163 </test> |
0
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
recetox
parents:
diff
changeset
|
164 <!-- The following test has different results on three platform I've tried --> |
328710890963
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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165 <!-- <test> |
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166 <param name="data" value="input_data_nobatch.csv" ftype="csv"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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167 <param name="mode" value="single_batch"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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168 <param name="wavelet_filter" value="d"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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169 <param name="filter_length" value="2"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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170 <param name="k" value="20"/> |
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171 <param name="alpha" value="0"/> |
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172 <param name="cutoff" value="0"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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173 <output name="normalized_data" file="normalized_data_nobatch.tsv"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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174 </test> --> |
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175 <test expect_failure="true"> |
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176 <param name="data" value="na_data.csv" ftype="csv"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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177 </test> |
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178 <test expect_failure="true"> |
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179 <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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180 </test> |
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181 </tests> |
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182 |
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183 <help> |
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184 <![CDATA[ |
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185 @HELP@ |
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186 ]]> |
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187 </help> |
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188 |
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189 <citations> |
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190 <citation type="doi">10.1016/j.aca.2019.02.010</citation> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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191 <citation type="doi">10.1007/s11306-021-01839-7</citation> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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192 </citations> |
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193 |
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194 </tool> |