view enasearch_retrieve_taxons.xml @ 2:92e869104274 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"

<tool id="enasearch_retrieve_taxons" name="Retrieve ENA taxon data" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
        <import>search_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="aggressive"><![CDATA[
enasearch
    retrieve_taxons
    @IDS@
    #if $result
        --result '$result'
    #end if
    @DISPLAY@
    $expanded
    $header
    --file '$output'
    --download 'txt'
    ]]></command>
    <inputs>
        <param argument="--ids" type="text" multiple="true" label="Ids for records to return"/>
        <param argument="--result" type="select" optional="true" label="Taxonomy result to return">
            <expand macro="taxonomy_results"/>
        </param>
        <expand macro="display_opt"/>
        <expand macro="expanded"/>
        <expand macro="header"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${ids}">
            <expand macro="change_format"/>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="ids" value="6543"/>
            <param name="result" value="sequence_release"/>
            <conditional name="display_opt">
                <param name="display" value="fasta"/>
            </conditional>
            <output name="output" ftype="fasta">
                <assert_contents>
                    <has_text text="Arion rufus partial 5.8S rRNA gene"/>
                    <has_text text="cytochrome c oxidase subunit I gene"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="ids" value="Human,Cat,Mouse,Zebrafish"/>
            <conditional name="display_opt">
                <param name="display" value="xml"/>
            </conditional>
            <output name="output" ftype="xml">
                <assert_contents>
                    <has_text text="taxon scientificName=&quot;Felis catus&quot;" />
                    <has_text text="taxon scientificName=&quot;Homo sapiens&quot;" />
                    <has_text text="taxon scientificName=&quot;Mus&quot;" />
                    <has_text text="taxon scientificName=&quot;Danio rerio&quot;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool retrieve ENA taxon data

See also [command line documentation](http://bebatut.fr/enasearch/cli_usage.html#enasearch-retrieve-taxons)
    ]]></help>
    <expand macro="citations"/>
</tool>