Mercurial > repos > ecology > obis_data
comparison robis.xml @ 0:1fcd81d65467 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
author | ecology |
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date | Thu, 18 Jan 2024 09:33:52 +0000 |
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-1:000000000000 | 0:1fcd81d65467 |
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1 <tool id="obis_data" name="OBIS occurences" version="@VERSION@" profile="20.01"> | |
2 <description>retrieve data</description> | |
3 <macros> | |
4 <import>macro.xml</import> | |
5 </macros> | |
6 <expand macro="topic"/> | |
7 <expand macro="requirements"> | |
8 <requirement type="package" version="2.11.3">r-robis</requirement> | |
9 </expand> | |
10 <required_files> | |
11 <include type="literal" path="robis.r"/> | |
12 </required_files> | |
13 <command detect_errors="exit_code"><![CDATA[ | |
14 Rscript | |
15 '$__tool_directory__/robis.r' | |
16 '$species' | |
17 '$taxon' | |
18 '$lat_min' | |
19 '$lat_max' | |
20 '$long_min' | |
21 '$long_max' | |
22 '$output' | |
23 ]]> | |
24 </command> | |
25 <inputs> | |
26 <param name="species" type="text" label="Scientific name of the species" help="Genus species format, eg : Scomber scombrus"> | |
27 <validator type="regex">^[A-Za-z ]*$</validator> | |
28 </param> | |
29 <param name="taxon" type="text" label="Taxon ID"> | |
30 <validator type="regex">^[0-9]*$</validator> | |
31 </param> | |
32 <param name="lat_min" type="float" min="-90" max="90" value="0" label="Input latitude min (+north/-south):" optional="true"/> | |
33 <param name="lat_max" type="float" min="-90" max="90" value="0" label="Input latitude max (+north/-south):" optional="true"/> | |
34 <param name="long_min" type="float" min="-90" max="90" value="0" label="Input longitude min (+east/-west):" optional="true"/> | |
35 <param name="long_max" type="float" min="-90" max="90" value="0" label="Input longitude max (+east/-west):" optional="true"/> | |
36 </inputs> | |
37 <outputs> | |
38 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> | |
39 </outputs> | |
40 <tests> | |
41 <test expect_num_outputs="1"> | |
42 <param name="species" value="Scomber scombrus"/> | |
43 <output name="output"> | |
44 <assert_contents> | |
45 <has_text text="Scombridae"/> | |
46 <has_n_columns n="163"/> | |
47 </assert_contents> | |
48 </output> | |
49 </test> | |
50 <test expect_num_outputs="1"> | |
51 <param name="lat_min" value="6"/> | |
52 <param name="lat_max" value="12"/> | |
53 <param name="long_min" value="40"/> | |
54 <param name="long_max" value="43"/> | |
55 <output name="output"> | |
56 <assert_contents> | |
57 <has_text text="basisOfRecord"/> | |
58 <has_n_columns n="144"/> | |
59 </assert_contents> | |
60 </output> | |
61 </test> | |
62 </tests> | |
63 <help><![CDATA[ | |
64 =========================== | |
65 Get species occurences data | |
66 =========================== | |
67 **What it does** | |
68 | |
69 Search and retrieve species occurences across OBIS database. | |
70 | |
71 | | |
72 | |
73 **How to use it** | |
74 | |
75 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Scomber scombrus. | |
76 | |
77 Or enter the latitude longitude of the area you want to retrieve data from. | |
78 | |
79 | |
80 | | |
81 | |
82 **Output** | |
83 | |
84 The tool returns a table with the species observations available in OBIS database. | |
85 | |
86 Output file will have at least the following attributes : BasisOfRecords, longitude, latitude, species, individualcount. | |
87 | |
88 | | |
89 | |
90 **How it works** | |
91 | |
92 This tool use the robis R package. | |
93 | |
94 | |
95 Includes functionality for retrieving species occurrence data, and combining those data. | |
96 ]]></help> | |
97 <expand macro="obis_doiref"/> | |
98 </tool> |