annotate make_eml.xml @ 0:9cbac7a9b1a3 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d139641e5afb8c75b8aded37bdbd7aecae0fb83

<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0">
    <description> Create EML from EAL templates</description>
    <requirements>
        <requirement type="package" version="4.3.1">r-base</requirement>
        <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    mkdir output_template &&
    #for $input in $templates
        ln -s '$input' 'output_template/${input.element_identifier}.txt';
    #end for
    Rscript 
		'$__tool_directory__/make_eml.R' 2> err.txt
		'title'
    ]]></command>
    <inputs>
        <param name="templates" type="data_collection"  collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection." />
		<param name="title" type="text" label="Title for your dataset." />
    </inputs>
    <outputs>
		 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
		 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2"> 
            <param name="templates">
                <collection type="list">
			<element name="annotations" value="annotations.txt"/>
                        <element name="keywords" value="keywords.txt" />
                        <element name="attributes_data_blary_al" value="attributes_data_blary_al.txt"/>
                        <element name="catvars_data_blary_al" value="catvars_data_blary_al.txt"/>
                        <element name="geographic_coverage" value="geographic_coverage.txt" />
                        <element name="personnel" value="personnel.txt" />
                </collection>
            </param>
            <output name="metadataout" >
			<assert_contents>
				<is_valid_xml />
				<xml_element path="./dataset"/>
                	</assert_contents>
            </output>
        </test>
    </tests>
<help><![CDATA[
.. class:: warningmark

'''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates.

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

This tool produce EML metadata from EAL templates.
This tool can be used in the continuation of the eml2eal tool.

**How to use it?**
--------------------
To use this tool, you can select, in your history a data collection with EAL templates made by the eml2eal tool. 
You can also select your own templates that you have to integrate into a Galaxy collection.

To do so you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click
on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.

 .. class:: infomark 
 
 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
 

You then have to select your collection in the upload box of the tool and click **Execute** to get your EML metadata.
]]></help>
</tool>