Mercurial > repos > ecology > cb_div
comparison div_index.xml @ 0:abc8da8c12ba draft
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author | ecology |
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date | Wed, 04 Jan 2023 13:21:41 +0000 |
parents | |
children | 5b31641e6d30 |
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1 <tool id="cb_div" name="Diversity" version="@VERSION@" profile = "20.01"> | |
2 <description>indicators</description> | |
3 <macros> | |
4 <import>macro.xml</import> | |
5 </macros> | |
6 <expand macro="cb_requirements"> | |
7 <requirement type="package" version="1.3.2">r-tidyverse</requirement> | |
8 <requirement type="package" version="1.7_20">r-ade4</requirement> | |
9 <requirement type="package" version="2.2">r-adiv</requirement> | |
10 <requirement type="package" version="3.4.0">r-ggplot2</requirement> | |
11 </expand> | |
12 <required_files> | |
13 <include type="literal" path="div_index.r"/> | |
14 </required_files> | |
15 <command detect_errors="exit_code"><![CDATA[ | |
16 Rscript | |
17 '$__tool_directory__/div_index.r' | |
18 '$input_data' | |
19 '$output_div' | |
20 '$output_rdata' | |
21 '$plots' | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param name="input_data" type="data" format="rdata" label="Input Clean data"/> | |
26 </inputs> | |
27 <outputs> | |
28 <data name="output_div" from_work_dir="Valeurs_stat.tabular" format="tabular" label="Diversity index"/> | |
29 <data name="output_rdata" from_work_dir="div_df.RDS" format="rdata" label="Diversity Rdata"/> | |
30 <collection type="list" name="plots" label="Diversity plot"> | |
31 <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> | |
32 </collection> | |
33 </outputs> | |
34 <tests> | |
35 <test expect_num_outputs="3"> | |
36 <param name="input_data" value="Clean_Rdata.rdata"/> | |
37 <output name="output_div"> | |
38 <assert_contents> | |
39 <has_n_columns n="20"/> | |
40 </assert_contents> | |
41 </output> | |
42 <output name="output_rdata"> | |
43 <assert_contents> | |
44 <has_text text="no"/> | |
45 </assert_contents> | |
46 </output> | |
47 <output_collection name="plots" type="list" count="14"/> | |
48 </test> | |
49 </tests> | |
50 <help><![CDATA[ | |
51 ==================== | |
52 Diversity indicators | |
53 ==================== | |
54 | |
55 | |
56 **What it does** | |
57 | |
58 Calculates the diversity indicators (Shannon, Simpson, ...). | |
59 | |
60 **Input description** | |
61 | |
62 Clean Rdata file from the previous tool Dissimilarity. | |
63 | |
64 +----------------+ | |
65 | Rdata | | |
66 +================+ | |
67 | Clean data | | |
68 +----------------+ | |
69 | ... | | |
70 +----------------+ | |
71 | |
72 | |
73 **Output** | |
74 | |
75 - 1 .RDS file | |
76 - 1 tabular file for all the diversity indices | |
77 - Multiple png plots one for each indices | |
78 | |
79 | |
80 | |
81 ]]> </help> | |
82 <expand macro="cb_bibref"/> | |
83 </tool> |