annotate get_feature_info.xml @ 5:234d7babf34b draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae

<tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.2">
    <description>using REST API</description>
    <requirements>
        <requirement type="package" version="2.12.4">requests</requirement>
        <requirement type="package" version="1.10.0">six</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
python '$__tool_directory__/get_feature_info.py'
-e $expand
-f $format_selector
-i '$input'
-s $species_selector
> '$output'
]]>
    </command>

    <inputs>
    <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
    <param name="species_selector" type="select" label="Select species">
        <option value="ensembl" selected="true">Vertebrates</option>
        <option value="ensemblgenomes">Other species</option>
    </param>
    <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" />
    <param name="format_selector" type="select" label="Output format">
        <option value="full" selected="true">Full</option>
        <option value="condensed">Condensed</option>
    </param>
    </inputs>

    <outputs>
        <data name="output" format="json" label="$(tool.name) on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="txt" value="input.txt" />
            <param name="expand" value="false" />
            <output name="output" ftype="json">
                <assert_contents>
                    <has_text text="ENSG00000157764" />
                    <has_text text="ENSG00000248378" />
                    <has_text text="homo_sapiens" />
                    <has_text text="protein_coding" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Retrieve feature information in JSON format from Ensembl using its REST API.

Uses the `"POST lookup/id"`_ API endpoint.

.. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post
]]>
    </help>
    <citations>
    </citations>
</tool>