Mercurial > repos > ecology > ecology_presence_abs_abund

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:16:26 +0000
parents f9bce5117161
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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diff changeset
1 <tool id="ecology_presence_abs_abund" name="Presence-absence and abundance" version="@VERSION@" profile="20.01">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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2 <description>Community abundance map, presence barplot and rarefaction curves</description>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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3 <macros>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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4 <import>macro.xml</import>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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5 </macros>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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6 <expand macro="Explo_requirements">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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7 <requirement type="package" version="2.5_7">r-vegan</requirement>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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8 </expand>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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9 <command detect_errors="exit_code"><![CDATA[
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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10 Rscript
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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11 '$__tool_directory__/graph_pres_abs_abund.r'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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12 '$input'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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13 '$colnames'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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14 #if $method.type=='abund':
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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15 'TRUE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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16 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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17 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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18 '$method.latitude'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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19 '$method.longitude'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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20 '$method.individual'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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21 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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22 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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23 '$method.species'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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24 #elif $method.type=='pres_abs':
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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25 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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26 'TRUE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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27 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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28 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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29 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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30 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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31 '$method.site'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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32 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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33 '$method.species'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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34 #else:
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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35 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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36 'FALSE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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37 'TRUE'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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38 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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39 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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40 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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41 ''
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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42 '$method.number'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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43 '$method.species'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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44 #end if
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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45 '$abundance'
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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46 ]]>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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47 </command>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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48 <inputs>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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49 <expand macro="explo_input"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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50 <conditional name="method">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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51 <param name="type" type="select" label="Variables presence, absence and abundance" display="radio">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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52 <option value="abund">Abundance map in the environment </option>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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53 <option value="pres_abs">Presence count of taxons (barplot)</option>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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54 <option value="rare">Rarefaction curve of species</option>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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55 </param>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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56 <when value="abund">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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57 <param name="latitude" label="Select column containing latitudes " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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58 <param name="longitude" label="Select column containing longitudes" type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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59 <param name="individual" type="text" label="What do you study in this analysis ?" help="Simply allows you to use any name you want in your plot's title (ex : ''Bats'', ''Chiroptera'')"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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60 <param name="species" label="Select column containing taxon " type="data_column" data_ref="input" numerical="false" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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61 </when>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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62 <when value="pres_abs">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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63 <param name="site" label="Select column containing your separation variable" type="data_column" help="ex : location, protection status, ..." data_ref="input" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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64 <param name="species" label="Select column containing taxon " type="data_column" data_ref="input" numerical="false" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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65 </when>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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66 <when value="rare">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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67 <param name="number" label="Size of subsamples" type="text" help="Rarefaction curves are calculated over random subsamples, you can choose the size you want depending on your data and the analysis you need. Should be smaller than the size of your community"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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68 <param name="species" label="Select column containing species " type="data_column" data_ref="input" numerical="false" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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69 </when>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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70 </conditional>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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71 <param name="abundance" label="Select column containing abundances " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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72 </inputs>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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73 <outputs>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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74 <data name="output_abund" from_work_dir="Data_abund.txt" format="txt" label="Data used">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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75 <expand macro="explo_filter_abund"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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76 </data>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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77 <data name="output_pres_abs" from_work_dir="Locations.txt" format="txt" label="Locations used">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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78 <expand macro="explo_filter_pres_abs"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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79 </data>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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80 <data name="output_rare" from_work_dir="Rare.tabular" format="tabular" label="Rare indice">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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81 <expand macro="explo_filter_rare"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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82 </data>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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83 <collection type="list" name="plots">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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84 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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85 </collection>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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86 </outputs>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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87 <tests>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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88 <test>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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89 <param name="input" value="Reel_life_survey_fish_modif2.tabular"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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90 <param name="colnames" value="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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91 <conditional name="method">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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92 <param name="abund" value="true"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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93 <param name="latitute" value="9"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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94 <param name="longitude" value="10"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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95 <param name="individual" value="fishes"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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96 <param name="species" value="15"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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97 </conditional>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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98 <param name="abundance" value="18"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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99 <output name="output_abund">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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100 <assert_contents>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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101 <has_n_lines n="12"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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102 </assert_contents>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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103 </output>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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104 <output_collection name="plots" type="list" count="1">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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105 <element name="mappy" ftype="png">
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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106 <assert_contents>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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107 <has_text text="PNG"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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108 </assert_contents>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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109 </element>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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110 </output_collection>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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111 </test>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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112 </tests>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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113 <expand macro="topic"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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114 <help><![CDATA[
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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115 =============================================================================
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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116 Map of community abundance, presence barplot of taxons and rarefaction curves
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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117 =============================================================================
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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118
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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119 **Map of community abundance**
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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120
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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121
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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122 This tool computes abundances of each taxon for each location and plots it according to longitude and latitude. Size of dots permits to get information on the abundance found at the location. Under 10 taxons, colors represents the different taxons and over 10 taxons it represents the abundance as well.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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123 Handy to get spatialized view of your abundances and see if some locations can pull results in a certain direction.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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124
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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125
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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126 Input description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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127
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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128
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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129 A tabular file with observation data. Must at least contain four columns abundance, latitude, longitude and taxon (any taxon level : species, family, ...).
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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130
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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131
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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132 +----------+-----------+---------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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133 | latitude | longitude | taxon | number |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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diff changeset
134 +==========+===========+=========+============+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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135 | lat |long | taxonID | 4 |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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136 +----------+-----------+---------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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137 | ... | ... | ... | ... |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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138 +----------+-----------+---------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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139
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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140
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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141 Output description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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142
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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143
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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144 A png file with every abundance dots for each location, a map without base.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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145 A text file containing the geographical range of the data.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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146
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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147
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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148 **Presence count of taxons (barplot)**
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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149
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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150
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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151 This tool computes the number of presence of each taxon according to a separation factor (ex: location, protection status, ...) and produces a barplot representing the relative presence count of each taxon. Handy to see the most ubiquitous taxons in the studied community.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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152 If more than 40 different taxons in the separations, plots are hard to read properly so they won't be produced. In that case you can cut your data into smaller parts to get several readable representations for one separation.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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153
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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154
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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155 Input description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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156
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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157
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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158 A tabular file with observation data. Must at least contain three columns species, abundance and the separation variable.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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159
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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160
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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161 +--------------+------------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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162 | species.code | variable | number |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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163 +==============+============+============+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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164 | speciesID | site | 4 |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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165 +--------------+------------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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166 | ... | ... | ... |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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167 +--------------+------------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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168
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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169
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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170 Output description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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171
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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172
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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173 A png file with barplots separated according to the variable and with multiple parts in different colors according to the different taxons.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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174
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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175
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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176 **Rarefaction curve of species**
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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177
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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178
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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179 This tool computes the rarefaction curves of each species. Permits you to assess species richness according to the number of samples. If there are more than 30 species in your data you will have one plot for each species and not all the curves on one plot.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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diff changeset
180 Using the R function rarefy (https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/rarefy).
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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181
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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182
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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183 Input description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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184
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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185
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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186 A tabular file with observation data. Must at least contain two columns abundance and species.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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187 A numeric value for the rarefaction indice (number of subsamples) must be entered.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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188
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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189
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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190 +-----------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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191 | species | number |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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192 +===========+============+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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193 | speciesID | 4 |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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194 +-----------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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195 | ... | ... |
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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196 +-----------+------------+
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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197
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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198
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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199 Output description :
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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200
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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201
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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202 A png file with one or multiple plots showing the rarefaction curves for each species according to the chosen rarefaction indice.
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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203 ]]> </help>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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204 <expand macro="book_bibref"/>
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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205
f9bce5117161 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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206 </tool>