Mercurial > repos > ecology > ecology_homogeneity_normality

annotate homogeneity_normality.xml @ 0:9f679060051a 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 16:56:15 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
1 <tool id="ecology_homogeneity_normality" name="Homoscedasticity and normality" version="@VERSION@" profile="20.01">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
2 <description>Checks the homogeneity of the variance and the normality of the distribution
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
3 </description>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
4 <macros>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
5 <import>macro.xml</import>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
6 </macros>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
7 <expand macro="Explo_requirements">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
8 <requirement type="package" version="3.0_10">r-car</requirement>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
9 <requirement type="package" version="1.1.1">r-cowplot</requirement>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
10 <requirement type="package" version="0.4.0">r-ggpubr</requirement>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
11 </expand>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
13 Rscript
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
14 '$__tool_directory__/graph_homogeneity_normality.r'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
15 '$input'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
16 '$colnames'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
17 '$date'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
18 '$species'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
19 '$variable'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
20 '$output_levene'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
21 '$output_ks'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
22 '$plots'
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
23 ]]>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
24 </command>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
25 <inputs>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
26 <expand macro="explo_input"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
27 <param name="date" label="Select column containing temporal data (year, date, ...)" type="data_column" data_ref="input" use_header_names="true"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
28 <param name="species" label="Select column containing species" type="data_column" data_ref="input" use_header_names="true"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
29 <param name="variable" label="Select column containing numerical values (like abundances)" type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
30 </inputs>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
31 <outputs>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
32 <data name="output_levene" from_work_dir="levene.txt" format="txt" label="Levene test - Homoscedasticity"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
33 <data name="output_ks" from_work_dir="ks.txt" format="txt" label="Kolmogorov-Smirnov test - Normality"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
34 <collection type="list" name="plots">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
35 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
36 </collection>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
37 </outputs>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
38 <tests>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
39 <test>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
40 <param name="input" value="data_frenchbbs.tabular"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
41 <param name="colnames" value="true"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
42 <param name="date" value="2"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
43 <param name="species" value="3"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
44 <param name="variable" value="4"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
45 <output name="output_levene" value="levene.txt"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
46 <output name="output_ks">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
47 <assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
48 <has_n_lines n="9"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
49 </assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
50 </output>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
51 <output_collection name="plots" type="list" count="2">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
52 <element name="Homogeneity" ftype="png">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
53 <assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
54 <has_text text="PNG"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
55 </assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
56 </element>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
57 <element name="Normal_distribution" ftype="png">
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
58 <assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
59 <has_text text="PNG"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
60 </assert_contents>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
61 </element>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
62 </output_collection>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
63 </test>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
64 </tests>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
65 <expand macro="topic"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
66 <help><![CDATA[
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
67 ===============================================================
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
68 Checks homogeneity of variance (homoscedasticity) and normality
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
69 ===============================================================
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
70
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
71
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
72 **What it does**
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
73
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
74
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
75 This tool checks homogeneity of variances (Levene test) for every species and represents it through multiple boxplots and the normal distribution (Kolmogorov-Smirnov test) represented by a distribution histogram and a Q-Q plot.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
76
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
77 If the levene test is significant (P-value in column Pr < 0.5 and at least one * at the end of the 4th line), variances aren't homogeneous, the hypothesis of *homoscedasticity is rejected*.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
78
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
79 If the K-S test is significant (p-value < 0.5), your numerical variable *isn't* normally distributed, the hypothesis of *normality is rejected*.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
80
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
81
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
82 **Input description**
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
83
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
84 A tabular file with observation data. Must at least contain three columns temporal referential (year, date, ...), species and a numerical factor.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
85
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
86 +----------+-----------+-----------+
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
87 | date | number | species |
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
88 +==========+===========+===========+
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
89 | year | 4 | speciesID |
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
90 +----------+-----------+-----------+
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
91 | ... | ... | ... |
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
92 +----------+-----------+-----------+
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
93
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
94 **Output**
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
95
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
96 A text output that summarizes the result of the performed Levene test for homogeneity of variances (homoscedasticity).
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
97
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
98 A text output that summarizes the result of the performed Kolmogrov-Smirnov test for normality.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
99
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
100 Multiple PNG files representing the homogeneity of variances for each species at each time point of the study.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
101
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
102 One PNG file representing the distribution of the data.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
103 ]]> </help>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
104 <expand macro="explo_bibref"/>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
105
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
106 </tool>