Mercurial > repos > ecology > ecology_stat_presence_abs

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:18:21 +0000
parents e5552099d0e3
children
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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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"
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2 <description>of a numeric variable</description>
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3 <macros>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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4 <import>macro.xml</import>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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5 </macros>
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6 <expand macro="Explo_requirements">
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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7 <requirement type="package" version="1.1.1">r-cowplot</requirement>
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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"
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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"
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10 </expand>
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11 <command detect_errors="exit_code"><![CDATA[
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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12 Rscript
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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13 '$__tool_directory__/graph_stat_presence_abs.r'
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14 '$input'
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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15 '$colnames'
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16 '$variable1'
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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17 '$species'
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18 '$location'
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19 '$time'
1
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20 '$__tool_directory__/functions.r'
0
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21 '$output_md'
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22 ]]>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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23 </command>
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24 <inputs>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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25 <expand macro="explo_input"/>
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26 <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"
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27 <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"
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28 <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"
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29 <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"
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30 </inputs>
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31 <outputs>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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32 <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"
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33 <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"
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34 </outputs>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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35 <tests>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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36 <test>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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37 <param name="input" value="Reel_life_survey_fish_modif.tabular"/>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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38 <param name="colnames" value="true"/>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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39 <param name="variable1" value="18"/>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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40 <param name="variable2" value="15"/>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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41 <output name="output_md" ftype="png">
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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42 <assert_contents>
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43 <has_text text="PNG"/>
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44 </assert_contents>
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45 </output>
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46 <output name="output_0" ftype="png">
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47 <assert_contents>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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48 <has_text text="PNG"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 </tests>
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53 <expand macro="topic"/>
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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54 <help><![CDATA[
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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55 ===================================================================================================================
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56 Create a boxplot, visualize the dispersion of a numeric variable and visualize correlation between species absences
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57 ===================================================================================================================
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58
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59
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60 **What it does**
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61
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62
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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63 This tool creates:
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64
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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65 - A boxplot of a numerical value (like the abundance) and a dispersion plot of this value according to a variable such as species.
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66
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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67 - 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.
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68
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69 Don't use datasets with too much species, it won't be readable.
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70
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71 **Input description**
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72
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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73 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.
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74
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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75 +-------------+------------+---------------+-------------+
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76 | number | time | species.code | location |
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77 +=============+============+===============+=============+
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78 | 2 | date | speciesID | site |
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79 +-------------+------------+---------------+-------------+
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80 | ... | ... | ... | ... |
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81 +-------------+------------+---------------+-------------+
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82
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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83 **Output**
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84
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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85 Two png files containing the three plots.
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86 ]]> </help>
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87 <expand macro="explo_bibref"/>
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88
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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89 </tool>