Mercurial > repos > ecology > cb_div
annotate div_index.xml @ 0:abc8da8c12ba draft
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author | ecology |
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date | Wed, 04 Jan 2023 13:21:41 +0000 |
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children | 5b31641e6d30 |
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> |
abc8da8c12ba
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> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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6 <expand macro="cb_requirements"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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7 <requirement type="package" version="1.3.2">r-tidyverse</requirement> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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8 <requirement type="package" version="1.7_20">r-ade4</requirement> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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9 <requirement type="package" version="2.2">r-adiv</requirement> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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10 <requirement type="package" version="3.4.0">r-ggplot2</requirement> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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11 </expand> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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12 <required_files> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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13 <include type="literal" path="div_index.r"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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14 </required_files> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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15 <command detect_errors="exit_code"><![CDATA[ |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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16 Rscript |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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17 '$__tool_directory__/div_index.r' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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18 '$input_data' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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19 '$output_div' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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20 '$output_rdata' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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21 '$plots' |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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22 ]]> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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23 </command> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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24 <inputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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25 <param name="input_data" type="data" format="rdata" label="Input Clean data"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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26 </inputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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27 <outputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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28 <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
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29 <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
parents:
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30 <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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31 <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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32 </collection> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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33 </outputs> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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34 <tests> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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35 <test expect_num_outputs="3"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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36 <param name="input_data" value="Clean_Rdata.rdata"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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37 <output name="output_div"> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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38 <assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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39 <has_n_columns n="20"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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40 </assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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41 </output> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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42 <output name="output_rdata"> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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43 <assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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44 <has_text text="no"/> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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45 </assert_contents> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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46 </output> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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47 <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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48 </test> |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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49 </tests> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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50 <help><![CDATA[ |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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51 ==================== |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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52 Diversity indicators |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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53 ==================== |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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54 |
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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 **What it does** |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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57 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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58 Calculates the diversity indicators (Shannon, Simpson, ...). |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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59 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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60 **Input description** |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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61 |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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62 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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63 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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64 +----------------+ |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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65 | Rdata | |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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66 +================+ |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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67 | Clean data | |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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68 +----------------+ |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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69 | ... | |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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70 +----------------+ |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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71 |
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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 **Output** |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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74 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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75 - 1 .RDS file |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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76 - 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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77 - Multiple png plots one for each indices |
abc8da8c12ba
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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78 |
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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 ]]> </help> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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82 <expand macro="cb_bibref"/> |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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83 </tool> |