view eml2eal.xml @ 6:6fc2341a92cb draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb

<tool id="eml2eal" name="EML to EAL" version="0.1.0+galaxy0" profile="22.05">
    <description> Create EAL templates from EML metadata </description>
    <requirements>
      <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       Rscript
         '$__tool_directory__/eml2eal.R'
         '$inputmetadatafile' &&
    find . -type f -empty -print -delete
    ]]></command>
    <inputs>
        <param name="inputmetadatafile" type="data" format="xml" label="EML metadata file" help="Insert only metadata using EML standard"/>
    </inputs>
    <outputs>
        <collection name="EML_templates" type="list" label="EML Templates">
            <discover_datasets pattern= "(?P&lt;designation&gt;.+)\.txt" format="tabular"/>
      </collection>
    </outputs>
    <tests>
         <test expect_num_outputs="1"> 
            <param name="inputmetadatafile" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
            <output_collection name="EML_templates" type="list">
                <element name="annotations" file="annotations.tabular" ftype="tabular"/>
                <element name="attributes_data_blary_al" file="attributes_data_blary_al.tabular" ftype="tabular"/>
                <element name="catvars_data_blary_al" file="catvars_data_blary_al.tabular" ftype="tabular"/>
                <element name="geographic_coverage" file="geographic_coverage.tabular" ftype="tabular" />
                <element name="keywords" file="keywords.tabular" ftype="tabular" />
                <element name="personnel" file="personnel.tabular" ftype="tabular" />
            </output_collection>
        </test>
    </tests>
<help><![CDATA[
.. class:: warningmark

'''TIP''' This tool requires metadata with **XML** format and using **EML** standard

**What it does?**
--------------------

This tool produce EAL templates from an EML metadata. These templates can be modified by the users by hand and reemplemented into Galaxy to reproduce an EML metadata with
the make_eml tool.

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

To use this tool, you have to upload a metadata written in XML and using EML standard.
By clicking the **Execute** button, the work will launch and you will be able to get your results in the historic on your right.
The results will be presented in a Galaxy Collection. You can then either download the files or you can edit them directly on Galaxy by selecting the *Visualize* icon
on the bottom of the templates outputs and and then selecting *Editor* in the list.
Once edited, this templates can me reassembled to produce a new EML with the **make_eml** tool in the EMLassemblyline tool section.

]]></help>
    <citations>
       <citation type="bibtex">@Manual{,
       title = {EMLassemblyline: A tool kit for building EML metadata workflows},
       author = {Colin Smith},
       year = {2022},
       note = {https://github.com/EDIorg/EMLassemblyline,
       https://ediorg.github.io/EMLassemblyline/},
       }</citation>
    </citations>
</tool>