Mercurial > repos > ecology > ecology_stat_presence_abs

comparison stat_presence_abs.xml @ 0:e5552099d0e3 draft

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
author ecology
date Tue, 27 Jul 2021 16:57:02 +0000
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children 9a2e0195bb43
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-1:000000000000 0:e5552099d0e3
1 <tool id="ecology_stat_presence_abs" name="Statistics on presence-absence" version="@VERSION@" profile = "20.01">
2 <description>of a numeric variable</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="Explo_requirements">
7 <requirement type="package" version="1.1.1">r-cowplot</requirement>
8 <requirement type="package" version="0.1.3">r-ggcorrplot</requirement>
9 <requirement type="package" version="1.0.5">r-dplyr</requirement>
10 </expand>
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript
13 '$__tool_directory__/graph_stat_presence_abs.r'
14 '$input'
15 '$colnames'
16 '$variable1'
17 '$species'
18 '$location'
19 '$time'
20 '$output_md'
21 ]]>
22 </command>
23 <inputs>
24 <expand macro="explo_input"/>
25 <param name="variable1" label="Select a column containing numerical values (such as the abundance) " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
26 <param name="species" label="Select the column of the x-axis : most commonly species" type="data_column" data_ref="input" use_header_names="true" help= "Variable for dispersion plot and to see the correlation between zeros"/>
27 <param name="location" label="Select column containing locations " type="data_column" data_ref="input" use_header_names="true"/>
28 <param name="time" label="Select column containing temporal data (year, date, ...) " type="data_column" data_ref="input" use_header_names="true"/>
29 </inputs>
30 <outputs>
31 <data name="output_md" from_work_dir="Med_Disp.png" format="png" label="Boxplot and dispersion plot"/>
32 <data name="output_0" from_work_dir="0_pb.png" format="png" label="Absence-correlation plot"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="input" value="Reel_life_survey_fish_modif.tabular"/>
37 <param name="colnames" value="true"/>
38 <param name="variable1" value="18"/>
39 <param name="variable2" value="15"/>
40 <output name="output_md" ftype="png">
41 <assert_contents>
42 <has_text text="PNG"/>
43 </assert_contents>
44 </output>
45 <output name="output_0" ftype="png">
46 <assert_contents>
47 <has_text text="PNG"/>
48 </assert_contents>
49 </output>
50 </test>
51 </tests>
52 <expand macro="topic"/>
53 <help><![CDATA[
54 ===================================================================================================================
55 Create a boxplot, visualize the dispersion of a numeric variable and visualize correlation between species absences
56 ===================================================================================================================
57
58
59 **What it does**
60
61
62 This tool creates:
63
64 - A boxplot of a numerical value (like the abundance) and a dispersion plot of this value according to a variable such as species.
65
66 - A correlation plot using the presence of zeros in the numerical value. Handy to see if there is a correlation between the absence of two species and suggest a co-dependency.
67
68 Don't use datasets with too much species, it won't be readable.
69
70 **Input description**
71
72 A tabular file with observation data. Must at least contain four columns a numerical value (ex: abundance), a temporal referential (year, date, ...), locations and species.
73
74 +-------------+------------+---------------+-------------+
75 | number | time | species.code | location |
76 +=============+============+===============+=============+
77 | 2 | date | speciesID | site |
78 +-------------+------------+---------------+-------------+
79 | ... | ... | ... | ... |
80 +-------------+------------+---------------+-------------+
81
82 **Output**
83
84 Two png files containing the three plots.
85 ]]> </help>
86 <expand macro="explo_bibref"/>
87
88 </tool>