comparison get_genetree.xml @ 2:950d9d11b6fb draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f

1:98aba0efe77a

<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">

                <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

            <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" ftype="json" />
        </test>
        <test>
            <param name="input_type" value="gene_tree_id" />
            <param name="input" value="ENSGT00390000003602" />
            <param name="output_format_selector" value="phyloxml" />

2:950d9d11b6fb

<tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.2">
    <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">

                <when value="none" />
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="2.12.4">requests</requirement>
        <requirement type="package" version="1.10.0">six</requirement>
    </requirements>
    <command>
<![CDATA[
python $__tool_directory__/get_genetree.py
--id_type $input_type

            <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" compare="sim_size" />
        </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" ftype="json" compare="sim_size" />
        </test>
        <test>
            <param name="input_type" value="gene_tree_id" />
            <param name="input" value="ENSGT00390000003602" />
            <param name="output_format_selector" value="phyloxml" />