Mercurial > repos > ecology > pampa_communitymetrics

annotate CalculateCommunityMetrics.xml @ 6:2cd0a5a321c2 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
author ecology
date Mon, 26 Apr 2021 16:05:03 +0000
parents 5bd7ddd7601f
children
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1 <tool id="pampa_communitymetrics" name="Calculate community metrics" version="@VERSION@">
ddd5b2e74b8b "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>
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3 <macros>
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4 <import>pampa_macros.xml</import>
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5 </macros>
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6 <expand macro="Pampa_requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript
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9 '$__tool_directory__/FunctExeCalcCommIndexesGalaxy.r'
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10 '$input'
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11 '$indexes'
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12 '$__tool_directory__/FunctPAMPAGalaxy.r'
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13 '$output_community'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <expand macro="pampa_input_calculate"/>
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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">
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19 <option selected="true" value="all">All</option>
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20 <option value="simpson.l">1-Simpson</option>
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21 <option value="pielou">Pielou</option>
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22 <option value="hill">Hill</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data name="output_community" from_work_dir="TabCommunityIndexes.tabular" format="tabular"/>
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27 </outputs>
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28 <tests>
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29 <test expect_num_outputs="1">
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30 <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
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31 <param name="indexes" value="all"/>
ddd5b2e74b8b "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"/>
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 </test>
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 </tests>
1
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35 <edam_topics>
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36 <edam_topic>topic_0610</edam_topic>
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37 <edam_topic>topic_3050</edam_topic>
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38 </edam_topics>
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39 <help><![CDATA[
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 ===============================================
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 Calculate community metrics from abundance data
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 ===============================================
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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43
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44 **What it does**
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45
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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46 This tool from PAMPA toolsuite computes community metrics from abundance data:
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47
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48 - Species richness / alpha diversity
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49 - Shannon index
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50 - Simpson index
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51 - Pielou index
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52 - Hill index
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53
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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54 |
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55
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56 **Input description**
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57
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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58 A tabular file with observation data. Must at least contain three columns 'observation.unit'
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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59 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.
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60
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61 +------------------+--------------+------------+
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62 | observation.unit | species.code | number |
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63 +==================+==============+============+
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64 | site_yearID | speciesID | 4 |
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65 +------------------+--------------+------------+
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66 | ... | ... | ... |
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67 +------------------+--------------+------------+
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68
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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69 OR
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70
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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71 +------+----------+--------------+------------+
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72 | year | location | species.code | number |
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73 +======+==========+==============+============+
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74 | 2000 |locationID| speciesID | 4 |
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75 +------+----------+--------------+------------+
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76 | ... | ... | ... | ... |
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77 +------+----------+--------------+------------+
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78
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79 The data frame may also contain:
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80
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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81 - 'size.class' field with 'G' representing big individuals in given species, 'M' middle-sized individuals and 'P' small individuals
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82 - 'rotation' field for STAVIRO data
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83
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84 |
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85
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86 **Output**
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87
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88 A tabular file with every metrics selected computed per observation unit
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89
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90 |
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91
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92 **Source**
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93
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94 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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95
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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96 ]]></help>
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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97
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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98 <expand macro="pampa_bibref" />
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99 </tool>