Mercurial > repos > ecology > pampa_presabs

annotate CalculatePresAbs.xml @ 0:c9dfe4e20a45 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 05:59:49 -0400
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children 5b45377f6a75
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c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 <tool id="pampa_presabs" name="Calculate presence absence table" version="@VERSION@">
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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2 <description>calculate presence absence table from observation data</description>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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'
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 <inputs>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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16 <expand macro="pampa_input_calculate"/>
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17 </inputs>
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18 <outputs>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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19 <data name="output_presabs" from_work_dir="TabPresAbs.tabular" format="tabular"/>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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"/>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 <output name="output_presabs" value="Presence_absence_table_sansszcl_cropped.tabular"/>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28 ====================================================
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29 Calculate presence absence table from abundance data
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 ====================================================
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31
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 **What it does**
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 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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35
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 |
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37
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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38 **Input description**
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39
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 A tabular file with observation data. Must at least contain three columns 'observation.unit'
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42
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43 +------------------+--------------+------------+
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44 | observation.unit | species.code | number |
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45 +==================+==============+============+
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46 | site_yearID | speciesID | 4 |
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47 +------------------+--------------+------------+
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48 | ... | ... | ... |
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49 +------------------+--------------+------------+
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50
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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51 OR
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52
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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53 +------+----------+--------------+------------+
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54 | year | location | species.code | number |
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55 +======+==========+==============+============+
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56 | 2000 |locationID| speciesID | 4 |
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57 +------+----------+--------------+------------+
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58 | ... | ... | ... | ... |
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59 +------+----------+--------------+------------+
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60
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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61 The data frame may also contain:
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62
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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63 - 'size.class' field with 'G' representing big individuals in given species, 'M'middle-sized individuals and 'P' small individuals
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64 - 'rotation' field for STAVIRO data
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66 |
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67
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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68 **Output**
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69
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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70
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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71 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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72
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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73
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74 |
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75
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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76 **Source**
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78 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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79
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80 ]]></help>
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81
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82 <expand macro="pampa_bibref" />
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83 </tool>