annotate vector_template.xml @ 3:40eb35199537 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063

<tool id="vector_template" name="Make templates for vector files" version="0.1.0+galaxy0" profile="22.05">
    <description>attributes for EML metadata creation</description>
    <requirements>
        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    
    #set $table = ""
    mkdir data_files && 
    
    #for $indata in $inputdata
        ln -s '$indata' 'data_files/${indata.element_identifier}';
        #set $table += $indata.element_identifier + " ";
    #end for
   
    Rscript 
         '$__tool_directory__/vector_templates.R'
         '$table'
         
    
    ]]></command>
    <inputs>
         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are vector files" help= "Input a data collection."/>
    </inputs>
    <outputs>
       <collection name="templates" type="list" label="Templates for vector data">
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.txt)" format="txt"/>
       </collection>
    </outputs>
    <tests>
        <test>
           <param name="inputdata">
              <collection type="list">
                 <element name="data_7.GeoJSON" value="data_7.GeoJSON"/>
              </collection>
           </param>
           <output_collection name='templates' type = "list" count="3"/>
        </test>
    </tests>
    <help><![CDATA[

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

This tool is used to produce EAL templates for data table used to build EML metadata. It produces the following eal files: 

- attibutes_my_vector.txt (describe the attributes of your vector file)
- catvars_my_vector.txt (only if there are one or more catégorical variable in your vector file)
- custom_units.txt (made to describe custom units if there are any)

After that, these files can be edited to add information about your vector file and then be used in the make eml tool to produce EML metadata.   

**How to use it?**
-------------------- 
        
To use this tool, you need to select, in your history a data collection with your vector data file(s) (format GeoJSON). 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*. To upload shapefile you need to create a composite data. 

.. class:: warningmark
        
'''TIP''' This tool dont accept as inputs composite data like shapefile at the moment. 

    ]]></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>