annotate BilanEnrichiRPen.xml @ 2:5ad79c210eb9 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro commit 4707473e9991d095310f475a54e041c95accd873

<tool id="vigiechiro_bilanenrichirp" name="Advanced restitution: 'Routier'or 'Pedestre' protocols" version="@VERSION@">
    <description>from Animal Detection on Acoustic Recordings</description>
    <macros>
        <import>vigiechiro_macros.xml</import>
    </macros>  
    <expand macro="vigiechiro_requirements">
        <expand macro="vigiechiro_bilanenrichi_requirements"/>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/BilanEnrichiRP.R' 
            '$idc2' 
            '$__tool_directory__/refRPSeuil50.csv' 
            '$__tool_directory__/SpeciesList.csv' 
        &&
	tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html &&
	tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html
]]>
    </command>
    <inputs>
        <param name="idc2" type="data" format="tabular" label="Corrected and validated observation file" help="Use output file from 'Tadarida identifications integration' : a sampling session file corrected and validated. Routier or Pedestre protocol"/>
        <param name="output_choice" type="select" label="Select a summarised or detailed display" multiple="true" optional="false" help="Chose whether your want a summarised or detailed display">
            <option value="detailed" selected="true">detailed output</option>
            <option value="summarised">summarised output</option>
        </param>		
    </inputs>
    <outputs>
        <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary table">
            <filter>'summarised' in output_choice</filter>
        </data>
        <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary html">
            <filter>'summarised' in output_choice</filter>
        </data>	 
        <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail table">
            <filter>'detailed' in output_choice</filter>
        </data>
        <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail html">
            <filter>'detailed' in output_choice</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="idc2" value="BilanEnrichiRP_Test1.tabular"/>
	    <param name="output_choice" value="detailed,summarised"/>
 	    <output name="output_detail_tabular" file="BilanEnrichiRP_Test1_out_tab.tabular" ftype="tabular"/>
 	    <output name="output_summary_tabular" file="BilanEnrichiRP_Test1_summarised.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

The tool analyzes the observations made with the "Routier" or "Pedestre" protocols.

**Arguments**

- Input is an observation/participation file corrected by the tools Tadarida data cleaner and Tadarida identifications integration.
- Outputs are Summary and details raw tabulars, and html visualisations.
    ]]></help>
    <expand macro="vigiechiro_bibref" />    
</tool>