Mercurial > repos > recetox > waveica

annotate macros.xml @ 7:1a2aeb8137bf draft

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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 425c0494ec2d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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1 <macros>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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2 <token name="@TOOL_VERSION@">0.2.0</token>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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3
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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4 <xml name="creator">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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5 <creator>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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6 <person
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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7 givenName="Maksym"
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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8 familyName="Skoryk"
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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9 url="https://github.com/maximskorik"
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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10 identifier="0000-0003-2056-8018" />
1
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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11 <person
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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12 givenName="Zargham"
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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13 familyName="Ahmad"
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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14 url="https://github.com/zargham-ahmad"
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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15 identifier="0000-0002-6096-224X" />
0
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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16 <organization
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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17 url="https://www.recetox.muni.cz/"
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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18 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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19 name="RECETOX MUNI" />
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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20 </creator>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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21 </xml>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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22
2
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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23 <xml name="annotation">
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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24 <xrefs>
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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25 <xref type="bio.tools">waveica</xref>
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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26 </xrefs>
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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27 </xml>
6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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28
1
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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29 <xml name="input_data">
b77023c41c76 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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30 <param type="data" name="data" label="Feature table" 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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31 </xml>
0
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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32 <xml name="general_parameters">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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33 <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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34 <param type="float" value="0" name="alpha" label="Alpha" help="trade-off value between the independence of samples (temporal ICA) and variables (spatial ICA), should be between 0 and 1"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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35 </xml>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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36 <xml name="batchwise_parameters">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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37 <param type="float" value="0.05" name="t" label="Batch-association threshold" help="threshold to consider a component associate with the batch,
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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38 should be between 0 and 1"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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39 <param type="float" value="0.05" name="t2" label="Group-association threshold" help="threshold to consider a component associate with the group,
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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40 should be between 0 and 1"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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41 </xml>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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42 <xml name="singlebatch_parameters">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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43 <param type="float" value="0" name="cutoff" label="Cutoff" help="threshold of the variation explained by the injection order for independent components, should be between 0 and 1"/>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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44 </xml>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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45 <xml name="exclude_blanks">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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46 <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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47 </xml>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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48 <xml name="wf">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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49 <conditional name="wf">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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50 <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="wavelet function and filter length [1] (see footnotes for more details)">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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51 <option value="d" selected="True">Daubechies</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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52 <option value="la" >Least Asymetric</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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53 <option value="bl" >Best Localized</option>
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54 <option value="c" >Coiflet</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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55 </param>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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56 <when value="d">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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57 <param name="wavelet_length" type="select" label="filter length">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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58 <option value="2" selected="True">2</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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59 <option value="4">4</option>
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60 <option value="6">6</option>
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61 <option value="8">8</option>
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62 <option value="10">10</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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63 <option value="12">12</option>
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64 <option value="14">14</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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65 <option value="16">16</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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66 <option value="18">18</option>
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67 <option value="20">20</option>
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68 </param>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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69 </when>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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70 <when value="la">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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71 <param name="wavelet_length" type="select" label="filter length">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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72 <option value="8">8</option>
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73 <option value="10">10</option>
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74 <option value="12">12</option>
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75 <option value="14">14</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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76 <option value="16">16</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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77 <option value="18">18</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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78 <option value="20">20</option>
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79 </param>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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80 </when>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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81 <when value="bl">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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82 <param name="wavelet_length" type="select" label="filter length">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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83 <option value="14">14</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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84 <option value="18">18</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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85 <option value="20">20</option>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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86 </param>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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87 </when>
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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88 <when value="c">
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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89 <param name="wavelet_length" type="select" label="filter length">
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90 <option value="6">6</option>
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91 <option value="12">12</option>
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92 <option value="18">18</option>
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93 <option value="24">24</option>
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94 <option value="30">30</option>
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95 </param>
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96 </when>
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97 </conditional>
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98 </xml>
7
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99 <xml name="split_output">
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100 <param name = "keep_two_output" label="Output metadata and data matrix as separate files" type="boolean" checked="false"
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101 truevalue="TRUE" falsevalue="FALSE" help="Keep two output files, one being the data matrix (feature table) and the second being the metadata table." />
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102 </xml>
0
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103
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104 <xml name="outputs">
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105 <outputs>
7
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106 <data name="normalized_data" format="tabular" label="Normalized table of ${on_string}">
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107 <change_format>
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108 <when input_dataset="data" attribute="ext" value="parquet" format="parquet" />
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109 </change_format>
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110 </data>
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111 <data name="metadata" format="tabular" label="Metadata table of ${on_string}">
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112 <filter>keep_two_output</filter>
4
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113 <change_format>
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114 <when input_dataset="data" attribute="ext" value="parquet" format="parquet" />
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115 </change_format>
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116 </data>
0
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117 </outputs>
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118 </xml>
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119
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120 <token name="@HELP@"><![CDATA[
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121 **Description**
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122
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123 Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis and independent
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124 component analysis. The WaveICA method uses the time trend of samples over the injection order, decomposes the
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125 original data into new multi-scale features, extracts and removes the batch effect resulting in normalized
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126 intensities across samples.
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127
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128 The input is an intensity-by-feature table with metadata in the following format:
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129
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130 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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131 | sampleName | class | sampleType | injectionOrder | batch | M85T34 | M86T41 | M86T518 | M86T539 | ... |
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132 +===============+========+============+================+=======+============+==============+=============+=============+=====+
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133 | VT_160120_002 | sample | sample | 1 | 1 | 228520.064 | 35646729.215 | 2386896.979 | 1026645.836 | ... |
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134 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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135 | QC1 | sample | QC | 2 | 1 | 90217.384 | 35735702.457 | 2456290.696 | 1089246.460 | ... |
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136 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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137 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
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138 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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139
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140
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141 + The required columns are **sampleName**, **class**, **sampleType**, **injectionOrder**, and the **features** that you want to normalize.
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142 + The **batch** column is required if batch correction mode is **Multiple batches** and optional otherwise.
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143 + The presence of any additional columns (except features) will result in incorrect batch correction or job failure.
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144 + the input table must not contain missing values. Missing intensities must be filled with 0.
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145 + **sampleType** column accepts three possible values: [QC, sample, blank] (case insensitive).
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146 + **class** column is used to denote a biological group of a sample (e.g., positive/negative species). The column accepts any values.
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147 + the **output** is the same table with corrected feature intensities.
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148
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149 .. rubric:: **Footnotes**
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150 .. [1] for details on wavelet-filter parameters refer to R `wavelets::wt.filter <https://www.rdocumentation.org/packages/wavelets/versions/0.3-0.2/topics/wt.filter>`_;
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151 .. [2] when using 'Multiple batches', please cite the WaveICA (2019) paper; else, cite WaveICA 2.0 (2021) paper;
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152 ]]>
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153 </token>
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154 </macros>