view Moyenne_geom.xml @ 0:a11841e270f3 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb

<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>