comparison draft_data_paper.xml @ 0:cfe884e53600 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292

0:cfe884e53600

<tool id="data_paper_from_EML" name="Make data paper sketches" version="0.1.0+galaxy0" profile="21.05">
    <description>from EML</description>
    <requirements>
       <requirement type="package" version="4.3.3">r-base</requirement>
       <requirement type="package" version="1.1.39">libxslt</requirement>
       <requirement type="package" version="3.5">pandoc</requirement>
       <requirement type="package" version="1.1.4">r-dplyr</requirement>
       <requirement type="package" version="2.11.2">r-mapview</requirement>
       <requirement type="package" version="1.4.6">r-xslt</requirement>
       <requirement type="package" version="1.3.6">r-xml2</requirement>
       <requirement type="package" version="2.1.1">phantomjs</requirement>
       
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    
    Rscript '$__tool_directory__/map_geographical_coverage.R' '$inputmetadatafile' &&
    
    xsltproc -o datapaper.html '$__tool_directory__/emldown_templates/bootstrap2.xsl' '${inputmetadatafile}' &&
    pandoc datapaper.html -o data_paper.docx
 
    ]]></command>
    <inputs>
       <param name="inputmetadatafile" type="data" format="xml" label="EML metadata file" help="Insert only metadata using EML standard"/>
    </inputs>
    <outputs>
        <data name="datapaper_docx" from_work_dir="data_paper.docx" format="docx" label="data_paper.docx"/>
    </outputs>
    <tests>
        <test>
            <param name="inputmetadatafile" value="EML.xml"/>
            <output name='datapaper_docx'>
                <assert_contents>
            	    <has_size value="31756" delta="50"/>
            	</assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    
**What it does?**
--------------------

This tool derived from the archived R Opensci emldown package thanks to French Fund for open science "OpenMetaPaper" project emldown R code improvements https://github.com/TanguyGen/emldown and creation fo the MetaShRIMPS R Shiny App <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents.

**How to use it?**
--------------------

You need to input an EML (Ecological Metadata Language) metadata file (xml format) and run the tool that will produce a draft of data paper in docx format that you can edit.  
    
    
    ]]></help>
    
    <citations>
           <citation type="bibtex">@misc{githubsurvey2023,
           author       = {Tanguy Genthon},
           title        = {{Metadata Shiny for Retroactive Information Management and Production of data paper Sketches}},
           publisher    = {Github},
           url          = {https://github.com/TanguyGen/metaCure},
           year         = {2023}
           }
          }</citation>
           <citation type="bibtex">@misc{githubsurvey2023b,
           author       = {Tanguy Genthon},
           title        = {{Produce beautifull website from EML}},
           publisher    = {Github},
           url          = {https://github.com/TanguyGen/emldown},
           year         = {2023}
           }
          }</citation>
    </citations>
</tool>