annotate CalculatePresAbs.xml @ 2:f1bfdeb5ebfe draft

"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
author ecology
date Mon, 27 Jul 2020 09:46:51 -0400
parents 5b45377f6a75
children 8d8aec182fb1
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1 <tool id="pampa_presabs" name="Calculate presence absence table" version="@VERSION@">
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2 <description>calculate presence absence table from observation 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 '$__tool_directory__/FunctExeCalcPresAbsGalaxy.r'
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10 '$input'
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11 '$__tool_directory__/FunctPAMPAGalaxy.r'
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12 '$output_presabs'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <expand macro="pampa_input_calculate"/>
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17 </inputs>
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18 <outputs>
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19 <data name="output_presabs" from_work_dir="TabPresAbs.tabular" format="tabular"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
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24 <output name="output_presabs" value="Presence_absence_table_sansszcl_cropped.tabular"/>
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25 </test>
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26 </tests>
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27 <edam_topics>
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28 <edam_topic>topic_0610</edam_topic>
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29 <edam_topic>topic_3050</edam_topic>
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30 </edam_topics>
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31 <help><![CDATA[
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32 ====================================================
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33 Calculate presence absence table from abundance data
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34 ====================================================
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36 **What it does**
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37
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38 This tool from PAMPA toolsuite computes an abundance (max and standard deviation if SVR data) and presence absence table at finest aggregation possible from observation data
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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39
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40 |
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 **Input description**
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43
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 A tabular file with observation data. Must at least contain three columns 'observation.unit'
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45 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.
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46
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47 +------------------+--------------+------------+
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48 | observation.unit | species.code | number |
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49 +==================+==============+============+
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50 | site_yearID | speciesID | 4 |
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51 +------------------+--------------+------------+
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52 | ... | ... | ... |
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53 +------------------+--------------+------------+
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54
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55 OR
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56
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57 +------+----------+--------------+------------+
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58 | year | location | species.code | number |
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59 +======+==========+==============+============+
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60 | 2000 |locationID| speciesID | 4 |
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61 +------+----------+--------------+------------+
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62 | ... | ... | ... | ... |
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63 +------+----------+--------------+------------+
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64
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65 The data frame may also contain:
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66
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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67 - 'size.class' field with 'G' representing big individuals in given species, 'M'middle-sized individuals and 'P' small individuals
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68 - 'rotation' field for STAVIRO data
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69
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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70 |
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71
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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72 **Output**
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73
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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74
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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75 A tabular file with presence/absence at finest aggregation available (per observation unit per species OR per observation unit per species per size class)
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76
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77
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78 |
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79
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80 **Source**
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81
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82 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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83
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84 ]]></help>
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85
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86 <expand macro="pampa_bibref" />
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87 </tool>