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comparison robis.xml @ 0:ed3688d04c12 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 13ac67c0a21d742b29e6273cdff058560abad770
author ecology
date Tue, 05 Nov 2024 14:17:28 +0000
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-1:000000000000 0:ed3688d04c12
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="167"/>
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="148"/>
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>