Mercurial > repos > ecology > pampa_communitymetrics

comparison CalculateCommunityMetrics.xml @ 0:ddd5b2e74b8b draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 06:00:10 -0400
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children e2b0eec4e788
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-1:000000000000 0:ddd5b2e74b8b
1 <tool id="pampa_communitymetrics" name="Calculate community metrics" version="@VERSION@">
2 <description>calculate community metrics from abundance data</description>
3 <macros>
4 <import>pampa_macros.xml</import>
5 </macros>
6 <expand macro="Pampa_requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript
9 '$__tool_directory__/FunctExeCalcCommIndexesGalaxy.r'
10 '$input'
11 '$indexes'
12 '$__tool_directory__/FunctPAMPAGalaxy.r'
13 '$output_community'
14 ]]>
15 </command>
16 <inputs>
17 <expand macro="pampa_input_calculate"/>
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">
19 <option selected="true" value="all">All</option>
20 <option value="simpson.l">1-Simpson</option>
21 <option value="pielou">Pielou</option>
22 <option value="hill">Hill</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="output_community" from_work_dir="TabCommunityIndexes.tabular" format="tabular"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
31 <param name="indexes" value="all"/>
32 <output name="output_community" value="Community_metrics_cropped.tabular"/>
33 </test>
34 </tests>
35 <help><![CDATA[
36 ===============================================
37 Calculate community metrics from abundance data
38 ===============================================
39
40 **What it does**
41
42 This tool from PAMPA toolsuite computes community metrics from abundance data:
43
44 - Specific richness
45 - Shannon index
46 - Simpson index
47 - Pielou index
48 - Hill index
49 - Relative richness
50
51 |
52
53 **Input description**
54
55 A tabular file with observation data. Must at least contain three columns 'observation.unit'
56 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.
57
58 +------------------+--------------+------------+
59 | observation.unit | species.code | number |
60 +==================+==============+============+
61 | site_yearID | speciesID | 4 |
62 +------------------+--------------+------------+
63 | ... | ... | ... |
64 +------------------+--------------+------------+
65
66 OR
67
68 +------+----------+--------------+------------+
69 | year | location | species.code | number |
70 +======+==========+==============+============+
71 | 2000 |locationID| speciesID | 4 |
72 +------+----------+--------------+------------+
73 | ... | ... | ... | ... |
74 +------+----------+--------------+------------+
75
76 The data frame may also contain:
77
78 - 'size.class' field with 'G' representing big individuals in given species, 'M' middle-sized individuals and 'P' small individuals
79 - 'rotation' field for STAVIRO data
80
81 |
82
83 **Output**
84
85 A tabular file with every metrics selected computed per observation unit
86
87 |
88
89 **Source**
90
91 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
92
93 ]]></help>
94
95 <expand macro="pampa_bibref" />
96 </tool>