annotate get_sequences.xml @ 4:3b686142e9c2 draft

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

<tool id="get_sequences" name="Get sequences 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_sequences.py'
-s $species_selector
--expand_3prime $expand_3prime
--expand_5prime $expand_5prime
-t $type_selector
-i '$input'
> '$output'
]]>
    </command>

    <inputs>
        <param name="input" type="data" format="txt" label="List of Ensembl 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_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
        <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
        <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR">
            <option value="genomic" selected="true">Genomic</option>
            <option value="cds">CDS</option>
            <option value="cdna">cDNA</option>
            <option value="protein">Protein</option>
        </param>
    </inputs>

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

    <tests>
          <test>
                <param name="input" ftype="txt" value="input.txt" />
                <param name="expand_3prime" value="0" />
                <param name="expand_5prime" value="0" />
                <param name="type_selector" value="genomic" />
                <output name="output" ftype="fasta">
                    <assert_contents>
                        <has_text text="ENSG00000157764" />
                        <has_text text="ENSG00000248378" />
                    </assert_contents>
            </output>
          </test>
     </tests>

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

Retrieves FASTA sequences from Ensembl using its REST API.

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

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