view data_manager/busco_fetcher.xml @ 4:828d961faea7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c

<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <description>dataset dowloader</description>
        <macros>
        <token name="@TOOL_VERSION@">5.8.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
        ## remove unwanted lineage folders and placement files
        ## https://gitlab.com/ezlab/busco/-/issues/784
        if [ -d '$out_file.extra_files_path'/lineages ]; then
            find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
        fi &&
        if [ -d '$out_file.extra_files_path'/placement_files ]; then
            find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
        fi &&
        ## unpack faa.gz files ready to use
        ## https://gitlab.com/ezlab/busco/-/issues/789
        if [ -d '$out_file.extra_files_path'/lineages ]; then
            find '$out_file.extra_files_path'/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
        fi
        && cp '$dmjson' '$out_file' 
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import datetime
    {
      "data_tables":{
        "busco_database":[
          {
            "value":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
            "name":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
            "version":"@TOOL_VERSION@",
            "path":"$out_file.extra_files_path"
          }
        ]
      }
    }]]>
            </configfile>
        </configfiles>
    <inputs>
        <param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
            <option value="all">All</option>
            <option value="prokaryota">Prokaryota</option>
            <option value="eukaryota">Eukaryota</option>
            <option value="virus">Virus</option>
        </param>
        <param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
            <option value="odb10" selected="true">OrthoDB 10</option>
            <option value="odb12">OrthoDB 12</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="lineage" value="virus"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="virus"/>
                    <has_text text="5.8.0"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>This tool downloads the BUSCO databases.</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv351</citation>
    </citations>
</tool>