Mercurial > repos > ecology > cb_div
annotate div_index.xml @ 1:5b31641e6d30 draft default tip
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
author | ecology |
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date | Sat, 18 Mar 2023 16:49:37 +0000 |
parents | abc8da8c12ba |
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rev | line source |
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0
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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1 <tool id="cb_div" name="Diversity" version="@VERSION@" profile = "20.01"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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2 <description>indicators</description> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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3 <macros> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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4 <import>macro.xml</import> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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5 </macros> |
1
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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6 <requirements> |
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abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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7 <requirement type="package" version="2.2">r-adiv</requirement> |
1
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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8 <requirement type="package" version="1.0.10">r-dplyr</requirement> |
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
ecology
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9 <requirement type="package" version="1.2.1">r-tidyr</requirement> |
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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10 <requirement type="package" version="3.1.8">r-tibble</requirement> |
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
ecology
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11 <requirement type="package" version="1.0.1">r-rgl</requirement> |
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
ecology
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12 </requirements> |
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abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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13 <required_files> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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14 <include type="literal" path="div_index.r"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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15 </required_files> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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16 <command detect_errors="exit_code"><![CDATA[ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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17 Rscript |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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18 '$__tool_directory__/div_index.r' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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19 '$input_data' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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20 '$output_div' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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21 '$output_rdata' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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22 '$plots' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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23 ]]> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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24 </command> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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25 <inputs> |
1
5b31641e6d30
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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26 <param name="input_data" type="data" format="rdata" label="Input clean data"/> |
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abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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27 </inputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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28 <outputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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29 <data name="output_div" from_work_dir="Valeurs_stat.tabular" format="tabular" label="Diversity index"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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30 <data name="output_rdata" from_work_dir="div_df.RDS" format="rdata" label="Diversity Rdata"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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31 <collection type="list" name="plots" label="Diversity plot"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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32 <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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33 </collection> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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34 </outputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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35 <tests> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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36 <test expect_num_outputs="3"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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37 <param name="input_data" value="Clean_Rdata.rdata"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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38 <output name="output_div"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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39 <assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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40 <has_n_columns n="20"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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41 </assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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42 </output> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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43 <output name="output_rdata"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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44 <assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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45 <has_text text="no"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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46 </assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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47 </output> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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48 <output_collection name="plots" type="list" count="14"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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49 </test> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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50 </tests> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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51 <help><![CDATA[ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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52 ==================== |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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53 Diversity indicators |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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54 ==================== |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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55 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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56 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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57 **What it does** |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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58 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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59 Calculates the diversity indicators (Shannon, Simpson, ...). |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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60 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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61 **Input description** |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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62 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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63 Clean Rdata file from the previous tool Dissimilarity. |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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64 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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65 +----------------+ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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66 | Rdata | |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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67 +================+ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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68 | Clean data | |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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69 +----------------+ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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70 | ... | |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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71 +----------------+ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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72 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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73 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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74 **Output** |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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75 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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76 - 1 .RDS file |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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77 - 1 tabular file for all the diversity indices |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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78 - Multiple png plots one for each indices |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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79 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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80 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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81 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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82 ]]> </help> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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83 <expand macro="cb_bibref"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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84 </tool> |