Mercurial > repos > ecology > cb_div
view 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 |
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<tool id="cb_div" name="Diversity" version="@VERSION@" profile = "20.01"> <description>indicators</description> <macros> <import>macro.xml</import> </macros> <expand macro="cb_requirements"> <requirement type="package" version="1.3.2">r-tidyverse</requirement> <requirement type="package" version="1.7_20">r-ade4</requirement> <requirement type="package" version="2.2">r-adiv</requirement> <requirement type="package" version="3.4.0">r-ggplot2</requirement> </expand> <required_files> <include type="literal" path="div_index.r"/> </required_files> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/div_index.r' '$input_data' '$output_div' '$output_rdata' '$plots' ]]> </command> <inputs> <param name="input_data" type="data" format="rdata" label="Input Clean data"/> </inputs> <outputs> <data name="output_div" from_work_dir="Valeurs_stat.tabular" format="tabular" label="Diversity index"/> <data name="output_rdata" from_work_dir="div_df.RDS" format="rdata" label="Diversity Rdata"/> <collection type="list" name="plots" label="Diversity plot"> <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> </collection> </outputs> <tests> <test expect_num_outputs="3"> <param name="input_data" value="Clean_Rdata.rdata"/> <output name="output_div"> <assert_contents> <has_n_columns n="20"/> </assert_contents> </output> <output name="output_rdata"> <assert_contents> <has_text text="no"/> </assert_contents> </output> <output_collection name="plots" type="list" count="14"/> </test> </tests> <help><![CDATA[ ==================== Diversity indicators ==================== **What it does** Calculates the diversity indicators (Shannon, Simpson, ...). **Input description** Clean Rdata file from the previous tool Dissimilarity. +----------------+ | Rdata | +================+ | Clean data | +----------------+ | ... | +----------------+ **Output** - 1 .RDS file - 1 tabular file for all the diversity indices - Multiple png plots one for each indices ]]> </help> <expand macro="cb_bibref"/> </tool>