annotate get_genetree/get_genetree.xml @ 0:f0018341e9f6 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty

<tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.1">
    <description>using REST API</description>
    <macros>
        <xml name="sequence_conditional">
            <conditional name="sequence">
                <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned">
                    <option value="protein" selected="true">Protein</option>
                    <option value="cdna">cDNA</option>
                    <option value="none">None</option>
                </param>
                <when value="protein">
                    <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" />
                    <yield />
                </when>
                <when value="cdna">
                    <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" />
                    <yield />
                </when>
                <when value="none" />
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="2.7">requests</requirement>
    </requirements>
    <command>
<![CDATA[
python $__tool_directory__/get_genetree.py
--id_type $input_type
-i "$input"
-g $species_selector
--format ${output_format.output_format_selector}
#if $output_format.output_format_selector == 'json'
    -s ${output_format.sequence.sequence_selector}
    #if $output_format.sequence.sequence_selector != 'none'
        -a ${output_format.sequence.aligned}
        -c ${output_format.sequence.cigar}
    #end if
#elif $output_format.output_format_selector == 'phyloxml'
    -s ${output_format.sequence.sequence_selector}
    #if $output_format.sequence.sequence_selector != 'none'
        -a ${output_format.sequence.aligned}
    #end if
#else
    --nh_format $output_format.nh_format
#end if
> "$output"
]]>
    </command>

    <inputs>
         <param name="input_type" type="select" label="Input type">
            <option value="gene_id" selected="true">Ensembl gene ID</option>
            <option value="gene_tree_id">Ensembl genetree ID</option>
        </param>
        <param name="input" type="text" label="Ensembl ID">
            <validator type="empty_field" />
        </param>
        <param name="species_selector" type="select" label="Select Species">
            <option value="ensembl" selected="true">Vertebrates</option>
            <option value="ensemblgenomes">Other species</option>
        </param>
        <conditional name="output_format">
            <param name="output_format_selector" type="select" label="Output format">
                <option value="json" selected="true">JSON</option>
                <!-- <option value="orthoxml">OrthoXML</option> -->
                <option value="phyloxml">phyloXML</option>
                <option value="nh">Newick</option>
            </param>
            <when value="json">
                <expand macro="sequence_conditional">
                    <param name="cigar" type="boolean" truevalue="1" falsevalue="0" label="Output the sequences also in CIGAR format" />
                </expand>
            </when>
            <when value="phyloxml">
                <expand macro="sequence_conditional" />
            </when>
            <when value="nh">
                <param name="nh_format" type="select" label="NH format" help="The format of a NH (New Hampshire) request">
                    <option value="simple" selected="true">simple</option>
                    <option value="full">full</option>
                    <option value="display_label_composite">display_label_composite</option>
                    <option value="species">species</option>
                    <option value="species_short_name">species_short_name</option>
                    <option value="ncbi_taxon">ncbi_taxon</option>
                    <option value="ncbi_name">ncbi_name</option>
                    <option value="njtree">njtree</option>
                    <option value="phylip">phylip</option>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" format="json" label="$(tool.name) on ${input_type} ${input}">
            <change_format>
                <when input="output_format.output_format_selector" value="phyloxml" format="phyloxml" />
                <when input="output_format.output_format_selector" value="nh" format="nhx" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input_type" value="gene_id" />
            <param name="input" value="ENSGALP00000027524" />
            <param name="output_format_selector" value="json" />
            <param name="sequence_selector" value="protein" />
            <param name="aligned" value="0" />
            <param name="cigar" value="0" />
            <output name="output" file="genetree.json" ftype="json" />
        </test>
        <test>
            <param name="input_type" value="gene_tree_id" />
            <param name="input" value="ENSGT00390000003602" />
            <param name="output_format_selector" value="json" />
            <param name="sequence_selector" value="protein" />
            <param name="aligned" value="0" />
            <param name="cigar" value="0" />
            <output name="output" file="genetree.json" fype="json" />
        </test>
        <test>
            <param name="input_type" value="gene_tree_id" />
            <param name="input" value="ENSGT00390000003602" />
            <param name="output_format_selector" value="phyloxml" />
            <param name="sequence_selector" value="protein" />
            <param name="aligned" value="0" />
            <output name="output" file="genetree.phyloxml" ftype="phyloxml" compare="sim_size" />
        </test>
    </tests>

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

Retrieve a gene tree from Ensembl using its REST API.

Uses the `"GET genetree/id"`_ and `"GET genetree/member/id"`_ API endpoint.

.. _"GET genetree/id": http://rest.ensembl.org/documentation/info/genetree
.. _"GET genetree/member/id": http://rest.ensembl.org/documentation/info/genetree_member_id
]]>
    </help>
    <citations>
    </citations>
</tool>