view enasearch_retrieve_data.xml @ 1:0719cfc3ebcb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

<tool id="enasearch_retrieve_data" name="Retrieve ENA data" version="@WRAPPER_VERSION@.0">
    <description>(other than taxon and project)</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_data
    @IDS@
    @DISPLAY@
    $expanded
    $header
    --file '$output'
    --download 'txt'
    ]]></command>
    <inputs>
        <param argument="--ids" type="text" multiple="true" label="Ids for records to return" help="Other than Taxon and Project. It can also be range of ids (e.g. ERA000010-ERA000020)"/>
        <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="ERA000010-ERA000020"/>
            <conditional name="display_opt">
                <param name="display" value="xml"/>
            </conditional>
            <output name="output" ftype="xml">
                <assert_contents>
                    <has_text text="SUBMISSION accession=&quot;ERA000011&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000012&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000013&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000014&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000015&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000016&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000017&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000018&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000019&quot;" />
                    <has_text text="SUBMISSION accession=&quot;ERA000020&quot;" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="ids" value="A00145"/>
            <conditional name="display_opt">
                <param name="display" value="fasta"/>
                <param name="range_start" value="3"/>
                <param name="range_stop" value="63"/>
            </conditional>
            <output name="output" ftype="fasta" md5="758cb77161dcf6f8cf841cb141e9277e"/>
        </test>
        <test>
            <param name="ids" value="AL513382"/>
            <conditional name="display_opt">
                <param name="display" value="text"/>
                <param name="offset" value="0"/>
                <param name="length" value="100"/>
            </conditional>
            <param name="expanded" value="true"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="ID   AL513382;" />
                </assert_contents>
            </output>
        </test>
<!--        <test>
            <param name="ids" value="PRJEB2772,AL513382"/>
            <conditional name="display_opt">
                <param name="display" value="html"/>
            </conditional>
            <param name="header" value="true"/>
            <output name="output" ftype="html" md5="7b23a8c12893728272f4993073e341f6"/>
        </test> this seems broken at the moment -->
    </tests>
    <help><![CDATA[
**What it does**

This tool retrieve ENA data (other than taxon and project)
    ]]></help>
    <expand macro="citations"/>
</tool>