Mercurial > repos > ecology > pampa_presabs
comparison CalculatePresAbs.xml @ 0:c9dfe4e20a45 draft
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author | ecology |
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date | Tue, 21 Jul 2020 05:59:49 -0400 |
parents | |
children | 5b45377f6a75 |
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1 <tool id="pampa_presabs" name="Calculate presence absence table" version="@VERSION@"> | |
2 <description>calculate presence absence table from observation 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 '$__tool_directory__/FunctExeCalcPresAbsGalaxy.r' | |
10 '$input' | |
11 '$__tool_directory__/FunctPAMPAGalaxy.r' | |
12 '$output_presabs' | |
13 ]]> | |
14 </command> | |
15 <inputs> | |
16 <expand macro="pampa_input_calculate"/> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="output_presabs" from_work_dir="TabPresAbs.tabular" format="tabular"/> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="input" value="ObservationsSansszcl_cropped.tabular"/> | |
24 <output name="output_presabs" value="Presence_absence_table_sansszcl_cropped.tabular"/> | |
25 </test> | |
26 </tests> | |
27 <help><![CDATA[ | |
28 ==================================================== | |
29 Calculate presence absence table from abundance data | |
30 ==================================================== | |
31 | |
32 **What it does** | |
33 | |
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 | |
35 | |
36 | | |
37 | |
38 **Input description** | |
39 | |
40 A tabular file with observation data. Must at least contain three columns 'observation.unit' | |
41 which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance. | |
42 | |
43 +------------------+--------------+------------+ | |
44 | observation.unit | species.code | number | | |
45 +==================+==============+============+ | |
46 | site_yearID | speciesID | 4 | | |
47 +------------------+--------------+------------+ | |
48 | ... | ... | ... | | |
49 +------------------+--------------+------------+ | |
50 | |
51 OR | |
52 | |
53 +------+----------+--------------+------------+ | |
54 | year | location | species.code | number | | |
55 +======+==========+==============+============+ | |
56 | 2000 |locationID| speciesID | 4 | | |
57 +------+----------+--------------+------------+ | |
58 | ... | ... | ... | ... | | |
59 +------+----------+--------------+------------+ | |
60 | |
61 The data frame may also contain: | |
62 | |
63 - 'size.class' field with 'G' representing big individuals in given species, 'M'middle-sized individuals and 'P' small individuals | |
64 - 'rotation' field for STAVIRO data | |
65 | |
66 | | |
67 | |
68 **Output** | |
69 | |
70 | |
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) | |
72 | |
73 | |
74 | | |
75 | |
76 **Source** | |
77 | |
78 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht. | |
79 | |
80 ]]></help> | |
81 | |
82 <expand macro="pampa_bibref" /> | |
83 </tool> |