Mercurial > repos > ecology > cb_div
comparison div_index.xml @ 0:abc8da8c12ba draft
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
| author | ecology |
|---|---|
| date | Wed, 04 Jan 2023 13:21:41 +0000 |
| parents | |
| children | 5b31641e6d30 |
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| -1:000000000000 | 0:abc8da8c12ba |
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| 1 <tool id="cb_div" name="Diversity" version="@VERSION@" profile = "20.01"> | |
| 2 <description>indicators</description> | |
| 3 <macros> | |
| 4 <import>macro.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="cb_requirements"> | |
| 7 <requirement type="package" version="1.3.2">r-tidyverse</requirement> | |
| 8 <requirement type="package" version="1.7_20">r-ade4</requirement> | |
| 9 <requirement type="package" version="2.2">r-adiv</requirement> | |
| 10 <requirement type="package" version="3.4.0">r-ggplot2</requirement> | |
| 11 </expand> | |
| 12 <required_files> | |
| 13 <include type="literal" path="div_index.r"/> | |
| 14 </required_files> | |
| 15 <command detect_errors="exit_code"><![CDATA[ | |
| 16 Rscript | |
| 17 '$__tool_directory__/div_index.r' | |
| 18 '$input_data' | |
| 19 '$output_div' | |
| 20 '$output_rdata' | |
| 21 '$plots' | |
| 22 ]]> | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="input_data" type="data" format="rdata" label="Input Clean data"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="output_div" from_work_dir="Valeurs_stat.tabular" format="tabular" label="Diversity index"/> | |
| 29 <data name="output_rdata" from_work_dir="div_df.RDS" format="rdata" label="Diversity Rdata"/> | |
| 30 <collection type="list" name="plots" label="Diversity plot"> | |
| 31 <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> | |
| 32 </collection> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test expect_num_outputs="3"> | |
| 36 <param name="input_data" value="Clean_Rdata.rdata"/> | |
| 37 <output name="output_div"> | |
| 38 <assert_contents> | |
| 39 <has_n_columns n="20"/> | |
| 40 </assert_contents> | |
| 41 </output> | |
| 42 <output name="output_rdata"> | |
| 43 <assert_contents> | |
| 44 <has_text text="no"/> | |
| 45 </assert_contents> | |
| 46 </output> | |
| 47 <output_collection name="plots" type="list" count="14"/> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help><![CDATA[ | |
| 51 ==================== | |
| 52 Diversity indicators | |
| 53 ==================== | |
| 54 | |
| 55 | |
| 56 **What it does** | |
| 57 | |
| 58 Calculates the diversity indicators (Shannon, Simpson, ...). | |
| 59 | |
| 60 **Input description** | |
| 61 | |
| 62 Clean Rdata file from the previous tool Dissimilarity. | |
| 63 | |
| 64 +----------------+ | |
| 65 | Rdata | | |
| 66 +================+ | |
| 67 | Clean data | | |
| 68 +----------------+ | |
| 69 | ... | | |
| 70 +----------------+ | |
| 71 | |
| 72 | |
| 73 **Output** | |
| 74 | |
| 75 - 1 .RDS file | |
| 76 - 1 tabular file for all the diversity indices | |
| 77 - Multiple png plots one for each indices | |
| 78 | |
| 79 | |
| 80 | |
| 81 ]]> </help> | |
| 82 <expand macro="cb_bibref"/> | |
| 83 </tool> |