Mercurial > repos > ecology > pampa_communitymetrics

annotate CalculateCommunityMetrics.xml @ 0:fd0c1dd5db33 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 09:58:37 +0000
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children 272517111a5d
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fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 <tool id="pampa_communitymetrics" name="Calculate community metrics" version="@VERSION@">
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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2 <description>calculate community metrics from abundance data</description>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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3 <macros>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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4 <import>pampa_macros.xml</import>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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5 </macros>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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6 <expand macro="Pampa_requirements"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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7 <command detect_errors="exit_code"><![CDATA[
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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8 Rscript
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 '$__tool_directory__/FunctExeCalcCommIndexesGalaxy.r'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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10 '$input'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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11 '$indexes'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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12 '$__tool_directory__/FunctPAMPAGalaxy.r'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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13 '$output_community'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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14 ]]>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 </command>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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16 <inputs>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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17 <expand macro="pampa_input_calculate"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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18 <param name="indexes" type="select" label="Choose the community metrics you want to compute" help="Presence/absence, Species richness, Simpson and Shannon index are systematically computed." multiple="true">
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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19 <option selected="true" value="all">All</option>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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20 <option value="simpson.l">1-Simpson</option>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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21 <option value="pielou">Pielou</option>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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22 <option value="hill">Hill</option>
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23 </param>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 </inputs>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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25 <outputs>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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26 <data name="output_community" from_work_dir="TabCommunityIndexes.tabular" format="tabular"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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27 </outputs>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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28 <tests>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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29 <test>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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31 <param name="indexes" value="all"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 <output name="output_community" value="Community_metrics_cropped.tabular"/>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 </test>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 </tests>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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35 <help><![CDATA[
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 ===============================================
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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37 Calculate community metrics from abundance data
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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38 ===============================================
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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39
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 **What it does**
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 This tool from PAMPA toolsuite computes community metrics from abundance data:
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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43
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 - Specific richness
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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45 - Shannon index
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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46 - Simpson index
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47 - Pielou index
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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48 - Hill index
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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49 - Relative richness
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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50
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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51 |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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52
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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53 **Input description**
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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54
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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55 A tabular file with observation data. Must at least contain three columns 'observation.unit'
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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56 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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57
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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58 +------------------+--------------+------------+
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59 | observation.unit | species.code | number |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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60 +==================+==============+============+
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61 | site_yearID | speciesID | 4 |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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62 +------------------+--------------+------------+
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63 | ... | ... | ... |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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64 +------------------+--------------+------------+
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65
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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66 OR
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67
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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68 +------+----------+--------------+------------+
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69 | year | location | species.code | number |
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70 +======+==========+==============+============+
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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71 | 2000 |locationID| speciesID | 4 |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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72 +------+----------+--------------+------------+
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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73 | ... | ... | ... | ... |
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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74 +------+----------+--------------+------------+
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75
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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76 The data frame may also contain:
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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77
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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78 - 'size.class' field with 'G' representing big individuals in given species, 'M' middle-sized individuals and 'P' small individuals
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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79 - 'rotation' field for STAVIRO data
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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80
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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81 |
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82
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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83 **Output**
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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84
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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85 A tabular file with every metrics selected computed per observation unit
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86
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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87 |
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88
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89 **Source**
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90
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91 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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92
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93 ]]></help>
fd0c1dd5db33 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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94
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95 <expand macro="pampa_bibref" />
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96 </tool>