Mercurial > repos > ecology > ecology_stat_presence_abs

annotate stat_presence_abs.xml @ 0:e5552099d0e3 draft

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