annotate data_manager/dfast.xml @ 1:23aec9361162 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dfast commit 5198e932e9ca2342f444c89f6e5fef619188191f

<tool id="data_manager_dfast" name="DFAST data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <macros>
        <token name="@TOOL_VERSION@">1.3.6</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">dfast</requirement>
    </requirements>
    <version_command>dfast --version | cut -d" " -f3</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir '$output_file.extra_files_path' &&
        wget https://dfast.annotation.jp/dfast_core_db.tar.gz &&
        tar -xvf dfast_core_db.tar.gz &&
        mv db/* '$output_file.extra_files_path'/ &&
        cp '$dmjson' '$output_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import datetime
#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
    {
      "data_tables":{
        "dfast":[
          {
            "value":"$version_id",
            "name":"DFAST DB from $version_id",
            "version":"$version_id",
            "path":"$output_file.extra_files_path"
          }
        ]
      }
    }]]></configfile>
    </configfiles>
    <inputs>
        <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <output name="output_file">
                <assert_contents>
                    <has_text text="DFAST DB"/>
                    <has_text text="dfast"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        This data managers fetches DFAST reference data from https://dfast.annotation.jp/
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.4054262</citation>
    </citations>
</tool>