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author | ecology |
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date | Sat, 25 Nov 2023 15:18:18 +0000 |
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<tool id="Mean_geom" name="Geometric means" version="0.1.0+galaxy0"> <description>- calcul of the geometric means for the "bois mort" indicator</description> <requirements> <requirement type="package" version="4.2.3">r-base</requirement> <requirement type="package" version="2.18.0.1">r-gdata</requirement> <requirement type="package" version="1.0.7">r-xlconnect</requirement> <requirement type="package" version="6.5-0">r-rms</requirement> <requirement type="package" version="1.1-3">r-mvtnorm</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/Moyenne_geom.r' '$input' '$separator' 'colnames' '$output1' '$output2' '$output3' '$output4' '$output5' '$output6' ]]></command> <inputs> <param name="input" type="data" format="csv,txt,tsv" label="Source file"/> <param name="separator" type="select" label="What character is the seprator in your data ?"> <option value = ",">Comma</option> <option value = "\t">Tab</option> <option value = ";">Semicolon</option> </param> <param name="colnames" type="boolean" label="The first line of your data represents the names of columns?"/> </inputs> <outputs> <data name="output1" from_work_dir="res2008_2012_scaled.csv" format="csv" label="res2008_2012_scaled.csv"/> <data name="output2" from_work_dir="res2013_2017_scaled.csv" format="csv" label="res2013_2017_scaled.csv"/> <data name="output3" from_work_dir="regres2008_2012_scaled.csv" format="csv" label="regres2008_2012_scaled.csv"/> <data name="output4" from_work_dir="regres2013_2017_scaled.csv" format="csv" label="regres2013_2017_scaled.csv"/> <data name="output5" from_work_dir="histo_data.tsv" format="tabular" label="histo_data.tsv"/> <data name="output6" from_work_dir="evolution_rate.tsv" format="tabular" label="evolution_rate.tsv"/> </outputs> <tests> <test> <param name='input' value="0_RESULTATS_BOIS_BIODIV_2021_V2.csv"/> <param name='separator' value="Comma"/> <param name='colnames' value="TRUE"/> <output name='output1' value="res2008_2012_scaled.csv"/> <output name='output2' value="res2013_2017_scaled.csv"/> <output name='output3' value="regres2008_2012_scaled.csv"/> <output name='output4' value="regres2013_2017_scaled.csv"/> <output name='output5' value="histo_data.tsv"/> <output name='output6' value="evolution_rate.tsv"/> </test> </tests> <help><![CDATA[ =================== **How to use it ?** =================== This tool takes in input a table or text or CSV file. Then you need to enter the separator of your data (comma, semicolon or tab) and indicates if your data has a header. Finally, run tools and it will produce some files with the result and a file with data to construct a bar plot of the result in the next step of the bois mort indicator workflow. ]]></help> </tool>