comparison div_index.xml @ 0:abc8da8c12ba draft

planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author ecology
date Wed, 04 Jan 2023 13:21:41 +0000
parents
children 5b31641e6d30
comparison
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-1:000000000000 0:abc8da8c12ba
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&lt;designation&gt;.+)\.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>