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comparison 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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-1:000000000000 0:c9dfe4e20a45
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>