Mercurial > repos > ecology > ecology_homogeneity_normality

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:16:46 +0000
parents 9f679060051a
children
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1 <tool id="ecology_homogeneity_normality" name="Homoscedasticity and normality" version="@VERSION@" profile="20.01">
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2 <description>Checks the homogeneity of the variance and the normality of the distribution
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3 </description>
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4 <macros>
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5 <import>macro.xml</import>
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6 </macros>
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7 <expand macro="Explo_requirements">
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8 <requirement type="package" version="3.0_10">r-car</requirement>
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9 <requirement type="package" version="1.1.1">r-cowplot</requirement>
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10 <requirement type="package" version="0.4.0">r-ggpubr</requirement>
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11 </expand>
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript
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14 '$__tool_directory__/graph_homogeneity_normality.r'
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15 '$input'
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16 '$colnames'
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17 '$date'
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18 '$species'
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19 '$variable'
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20 '$output_levene'
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21 '$output_ks'
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22 '$plots'
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23 ]]>
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24 </command>
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25 <inputs>
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26 <expand macro="explo_input"/>
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27 <param name="date" label="Select column containing temporal data (year, date, ...)" type="data_column" data_ref="input" use_header_names="true"/>
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28 <param name="species" label="Select column containing species" type="data_column" data_ref="input" use_header_names="true"/>
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29 <param name="variable" label="Select column containing numerical values (like abundances)" type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
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30 </inputs>
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31 <outputs>
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32 <data name="output_levene" from_work_dir="levene.txt" format="txt" label="Levene test - Homoscedasticity"/>
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33 <data name="output_ks" from_work_dir="ks.txt" format="txt" label="Kolmogorov-Smirnov test - Normality"/>
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34 <collection type="list" name="plots">
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35 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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36 </collection>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" value="data_frenchbbs.tabular"/>
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41 <param name="colnames" value="true"/>
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42 <param name="date" value="2"/>
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43 <param name="species" value="3"/>
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44 <param name="variable" value="4"/>
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45 <output name="output_levene" value="levene.txt"/>
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46 <output name="output_ks">
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47 <assert_contents>
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48 <has_n_lines n="9"/>
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49 </assert_contents>
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50 </output>
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51 <output_collection name="plots" type="list" count="2">
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52 <element name="Homogeneity" ftype="png">
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53 <assert_contents>
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54 <has_text text="PNG"/>
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55 </assert_contents>
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56 </element>
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57 <element name="Normal_distribution" ftype="png">
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58 <assert_contents>
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59 <has_text text="PNG"/>
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60 </assert_contents>
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61 </element>
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62 </output_collection>
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63 </test>
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64 </tests>
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65 <expand macro="topic"/>
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66 <help><![CDATA[
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67 ===============================================================
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68 Checks homogeneity of variance (homoscedasticity) and normality
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69 ===============================================================
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70
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71
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72 **What it does**
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73
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74
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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.
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76
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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*.
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78
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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*.
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80
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81
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82 **Input description**
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83
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84 A tabular file with observation data. Must at least contain three columns temporal referential (year, date, ...), species and a numerical factor.
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85
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86 +----------+-----------+-----------+
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87 | date | number | species |
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88 +==========+===========+===========+
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89 | year | 4 | speciesID |
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90 +----------+-----------+-----------+
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91 | ... | ... | ... |
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92 +----------+-----------+-----------+
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94 **Output**
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96 A text output that summarizes the result of the performed Levene test for homogeneity of variances (homoscedasticity).
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97
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98 A text output that summarizes the result of the performed Kolmogrov-Smirnov test for normality.
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99
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100 Multiple PNG files representing the homogeneity of variances for each species at each time point of the study.
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101
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102 One PNG file representing the distribution of the data.
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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103 ]]> </help>
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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104 <expand macro="explo_bibref"/>
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105
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106 </tool>