annotate data_manager/install_clair3_models.xml @ 0:11e42265a9b0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_clair3_models commit 2672414472cc968c736dc7d42f5a119ff8c16c62

<tool id="data_manager_clair3_models" name="Clair3 model downloader" version="0.0.1" tool_type="manage_data" profile="23.2">
    <requirements>
        <requirement type="package" version="3.12">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
            ## this code looks up the existing table and uses it to build a list of known models
            ## because models are uniquely identified by their name, downloading duplicate models
            ## would be an error, so it is useful to know which models we already have
            ##
            ## $__app__.tool_data_tables is a dictionary where the keys are data table names and the values 
            ## are TabularToolDataTable objects (from lib/galaxy/tools/data/__init__.py)
            ##
            ## the get_fields() method on the TabularToolDataTable returns a list of lists, with one list
            ## per line of the tool data table, so row[0] is the first field (i.e. the value column)
            ##

            #set $data_table = $__app__.tool_data_tables.get("clair3_models")
            #if $data_table is not None and len($data_table.get_fields()) > 0:
                #set $known_models = ','.join([ row[0] for row in $data_table.get_fields() ])
                #set $sha256_sums = ','.join([ row[1] for row in $data_table.get_fields() ])
            #else
                #set $known_models = None
                #set $sha256_sums = None
            #end if

        python '$__tool_directory__/model_fetcher.py'
            '${output_file}'
            #if $known_models is not None
                --known_models '$known_models'
                --sha256_sums '$sha256_sums'
            #end if
            #if $model_selection.source == 'latest'
                --download_latest
            #elif $model_selection.source == 'chosen'
                --download_models '$model_selection.model_list'
            #end if
    ]]></command>
    <inputs>
        <conditional name="model_selection">
            <param name="source" label="Select the source of the list of models to download" type="select">
                <option value="latest">Latest models from Rerio page</option>
                <option value="chosen">User provided list of models</option>
            </param>
            <when value="latest">
            </when>
            <when value="chosen">
                <param name="model_list" type="text" label="List of models to download" help="A comma separated list of model to download, e.g. 'r1041_e82_400bps_sup_v430,r1041_e82_400bps_hac_v430'">
                    <validator type="regex" message="Invalid model list. Format is a comma separated list of model names (e.g. 'r1041_e82_400bps_sup_v430,r1041_e82_400bps_hac_v430')">^[a-z_0-9,]+$</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json" label="Data Manager Output (JSON)" />
    </outputs>
    <tests>
        <test> <!-- test1 -->
            <conditional name="model_selection">
                <param name="source" value="chosen"/>
                <param name="model_list" value="r1041_e82_400bps_sup_v500,r1041_e82_400bps_hac_v500" />
            </conditional>
            <output name="output_file">
                <assert_contents>
                    <!-- the text 'r1041_e82_400bps_sup_v500' is only there if the test is run for the first time (i.e. empty test-data/clair3_models.loc) so need to look for something else -->
                    <has_text text='clair3_models' />
                </assert_contents>
            </output>
        </test>
        <test> <!-- test2 -->
            <conditional name="model_selection">
                <param name="source" value="latest"/>
            </conditional>
            <output name="output_file">
                <assert_contents>
                    <!-- because we don't know what the names of the latest models are we can only test to see if the data table output is created -->
                    <has_text text='data_tables' />  
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    Clair3_ is a variant caller for long read data developed at the University of Hong Kong. This tool makes use of models trained to match particular
    sequencing technologies and basecallers. Oxford Nanopore provides a set of models for Clair3 on their Rerio_ page. These tools are designed for
    "research release" under the terms of the "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" license_. This data manager allows
    downloading model files from the Rerio page and installing them on a Galaxy server.

    .. _Clair3: https://github.com/HKU-BAL/Clair3
    .. _Rerio: https://github.com/nanoporetech/rerio
    .. _license: https://github.com/nanoporetech/rerio/blob/master/LICENCE.txt
    ]]>
    </help>
    <citations>
        <citation type="doi">10.1101/2021.12.29.474431v2</citation>
        <citation type="bibtex"><![CDATA[@misc{ONT2024,
            title        = {Rerio},
            author       = {Oxford Nanopore Technologies},
            year         = 2024,
            howpublished = {\url{https://github.com/nanoporetech/rerio}},
            commit       = {c0c8ce6}
    }]]></citation>
    </citations>
</tool>