annotate cb_dissimilarity.xml @ 0:7e6cc3da1189 draft

planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
author ecology
date Fri, 02 Dec 2022 16:13:18 +0000
parents
children ffaa9a71b2d2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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1 <tool id="cb_dissim" name="Dissimilarity" version="@VERSION@" profile = "20.01">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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2 <description>indicator</description>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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3 <macros>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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4 <import>macro.xml</import>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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5 </macros>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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6 <expand macro="cb_requirements">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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7 <requirement type="package" version="2.16">r-rmarkdown</requirement>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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8 <requirement type="package" version="0.2.4">r-officedown</requirement>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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9 <requirement type="package" version="2.6_2">r-vegan</requirement>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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10 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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11 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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12 </expand>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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13 <required_files>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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14 <include type="literal" path="test-data/champbloc_qecb.csv"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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15 <include type="literal" path="test-data/ficheterrain.csv"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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16 <include type="literal" path="cb_dissimilarity.r"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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17 </required_files>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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18 <command detect_errors="exit_code"><![CDATA[
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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19 Rscript
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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20 '$__tool_directory__/cb_dissimilarity.r'
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21 '$fiche_val'
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22 '$input_data'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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23 '$choice'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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24 '$choice_date'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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25 '$output_qecb'
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26 '$output_eco'
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27 '$output_matri'
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28 '$plots_bf'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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29 '$plots_bm'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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30 '$plots'
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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31 ]]>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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32 </command>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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33 <inputs>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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34 <expand macro="cb_input"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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35 <param name="input_data" type="data" format="data" label="Input champbloc_qecb.csv"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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36 <param name="choice" type="select" display="radio" label="Do you have data after the year 2021?">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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37 <option value="N">No</option>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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38 <option value="Y">Yes</option>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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39 </param>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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40 <param name="choice_date" type="integer" value="2021" label="Until when do you have data (write only the YEAR) ?" help="Example write : 2021 "/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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41 </inputs>
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42 <outputs>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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43 <data name="output_qecb" from_work_dir="qecbnato0.RDS" format="Rdata" label="Clean Rdata"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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44 <data name="output_eco" from_work_dir="bret_egmp_basq_qecb.RDS" format="Rdata" label="Bret Rdata"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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45 <data name="output_matri" from_work_dir="matri_full.RDS" format="Rdata" label="Matrice full Rdata"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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46 <collection type="list" name="plots_bf" label="Bloc fixe et bloc mobile face sup plot">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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47 <discover_datasets pattern="bm(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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48 </collection>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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49 <collection type="list" name="plots_bm" label="Bloc mobile face sup et face inf plot">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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50 <discover_datasets pattern="fs(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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51 </collection><!--&lowbar; pour underscore-->
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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52 <collection type="list" name="plots" label="Distance plot">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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53 <discover_datasets pattern="distance(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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54 </collection>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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55 </outputs>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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56 <tests>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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57 <test expect_num_outputs="6">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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58 <param name="fiche_val" value="ficheterrain.csv"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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59 <param name="input_data" value="champbloc_qecb.csv"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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60 <param name="choice" value="N"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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61 <param name="choice_date" value="2021"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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62 <output name="output_qecb">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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63 <assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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64 <has_text text="E6P"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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65 </assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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66 </output>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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67 <output name="output_eco">
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68 <assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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69 <has_text text="6t"/>
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70 </assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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71 </output>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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72 <output name="output_matri">
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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73 <assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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74 <has_text text="6t"/>
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75 </assert_contents>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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76 </output>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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77 <output_collection name="plots_bf" type="list" count="23"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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78 <output_collection name="plots_bm" type="list" count="23"/>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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79 <output_collection name="plots" type="list" count="2"/>
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80 </test>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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81 </tests>
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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82 <help><![CDATA[
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83 =======================
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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84 Dissimilarity indicator
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85 =======================
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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86
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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87
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88 **What it does**
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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89
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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90 This tool computes the the Boulder Field Ecological Quality Index (BFEQ) based on biotic and abiotic variables that respond to the disturbance "boulder turning".
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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91
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92 **Input description**
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93
7e6cc3da1189 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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94 One input files in Rdata format.
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95
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96 +----------------+
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97 | Rdata |
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98 +================+
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99 | clean Rdata |
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100 +----------------+
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101 | ... |
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102 +----------------+
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105 **Output**
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107 - .RDS file 1 of them to use as an input for diversity index
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108 - Multiple png plots one for each of the locations
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111
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112 ]]> </help>
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113 <expand macro="cb_bibref"/>
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114 </tool>