annotate data_manager/pangolin_data_dm.xml @ 1:c22f6c820658 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa

<tool id="data_manager_pangolin_data" name="pangolin-data data manager" version="0.0.1+galaxy1" tool_type="manage_data" profile="20.01">
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.10">python</requirement>
        <requirement type="package" version="22.1.2">pip</requirement>
        <requirement type="package" version="2.28.1">requests</requirement>
        <requirement type="package" version="2.37.1">git</requirement>
        <requirement type="package" version="3.2.0">git-lfs</requirement>
        <requirement type="package" version="3.1.27">gitpython</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    #set $dt_names = []
    #if str($pangolin_data.enable) == "latest" or str($pangolin_data.enable) == "versions" 
        #set $dt_names = $dt_names + ["pangolin_data"]
    #end if
    #if str($pangolin_constellations.enable) == "latest" or str($pangolin_constellations.enable) == "versions"
        #set $dt_names = $dt_names + ["pangolin_constellations"]
    #end if
    #if str($pangolin_assignment.enable) == "latest" or str($pangolin_assignment.enable) == "versions"
        #set $dt_names = $dt_names + ["pangolin_assignment"]
    #end if
    #for $dt_name in $dt_names
        #set $data_table = $__app__.tool_data_tables.get($dt_name)
        #if $data_table is not None and len($data_table.get_fields()) != 0
            #set $known_revisions = '--known_revisions=' + ','.join([row[0] for row in $data_table.get_fields()])
        #else
            #set $known_revisions = ''
        #end if
        python '$__tool_directory__/pangolin_data_dm.py'
            $known_revisions
            #if $getVar($dt_name).enable == "latest"
                --latest
            #else if $getVar($dt_name).enable == "versions"
                --version_compatibility_file '$getVar($dt_name).compatibility_file'
                --versions=$getVar($dt_name).versions
            #end if
            '$dt_name'
            datatable_cache.json
            '${output_file}' &&
        #end for
        cp datatable_cache.json '${output_file}'
    ]]></command>
    <inputs>
        <expand macro="download_conditional" dt_name="pangolin_data" database_name="pangolin-data" software_name="pangolin" />
        <expand macro="download_conditional" dt_name="pangolin_constellations" database_name="constellations" software_name="scorpio" />
        <expand macro="download_conditional" dt_name="pangolin_assignment" database_name="pangolin-assignment" software_name="pangolin" />
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="pangolin_data">
                <param name="enable" value="versions" />
                <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
                <param name="versions" value="1.12" />
            </conditional>
            <conditional name="pangolin_constellations">
                <param name="enable" value="versions" />
                <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
                <param name="versions" value="0.1.10" />
            </conditional>
            <conditional name="pangolin_assignment">
                <param name="enable" value="no" />
            </conditional>
            <output name="output_file">
                <assert_contents>
                    <has_text text="pangolin-data v1.12" />
                    <has_text text='"description": "constellations release v0.1.10"' />
                    <has_text text='"min_scorpio_version": "0.3.17"' />
                    <not_has_text text='"description": "pangolin-assignment' />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="pangolin_data">
                <param name="enable" value="no" />
            </conditional>
            <conditional name="pangolin_constellations">
                <param name="enable" value="no" />
            </conditional>
            <conditional name="pangolin_assignment">
                <param name="enable" value="versions" />
                <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
                <param name="versions" value="1.12" />
            </conditional>
            <output name="output_file">
                <assert_contents>
                    <has_text text='"value": "v1.12"' />
                    <has_text text='"min_pangolin_version": "4"' />
                    <not_has_text text='"description": "constellations' />
                    <not_has_text text='"description": "pangolin-data' />
                </assert_contents>
            </output>
        </test>
        <test expect_failure="true">
            <conditional name="pangolin_data">
                <param name="enable" value="no" />
            </conditional>
            <conditional name="pangolin_constellations">
                <param name="enable" value="no" />
                <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
                <param name="versions" value="0.0.40" />
            </conditional>
            <conditional name="pangolin_assignment">
                <param name="enable" value="no" />
            </conditional>
        </test>
    </tests>
    <help><![CDATA[
        This data managers fetches models (from the pangolin-data_,
        pangolin-assignment_ and constellations_ repositories) for the
        pangolin_ SARS-CoV-2 lineage typing tool and updates the pangolin_data,
        pangolin_assignment and pangolin_constellations data tables.

        The default is to fetch the latest version of the databases. If specific versions of databases
        need to be installed, a version compatibility matrix needs to be provided to help choose
        the versions available. This matrix is stored in a CSV file in the pangolin repository
        and can be downloaded at this link_. When loading this file into Galaxy, the csv datatype
        needs to be selected, because the automatic format detection code detects this file as type txt.

        **Note** that this data manager will only download database versions mentioned in the above
        mentioned file. While effort is taken to ensure that this file is updated with each pangolin
        database release, if that has not happened, the user of this data manager will need to provide
        their own version compatibility matrix file in order to load the latest database release into Galaxy.

        The data manager will read the existing data tables and not re-download or replace databases
        that are already present in those data tables.

        .. _pangolin-data: https://github.com/cov-lineages/pangolin-data
        .. _pangolin-assignment: https://github.com/cov-lineages/pangolin-assignment
        .. _constellations: https://github.com/cov-lineages/constellations
        .. _pangolin: https://github.com/cov-lineages/pangolin
        .. _link: https://raw.githubusercontent.com/cov-lineages/pangolin/master/pangolin/data/data_compatibility.csv
    ]]></help>
    <citations>
        <citation type="doi">10.1093/ve/veab064</citation>
    </citations>
</tool>