comparison data_manager/data_manager_deeparg.xml @ 0:4a72de3780aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_deeparg commit 068be9bb0973bc877457d13d0d5a7c26a6cc1f96

0:4a72de3780aa

<tool id="data_manager_deeparg" name="Download data for DeepARG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.4</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">deeparg</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path' &&
        deeparg download_data -o '$out_file.extra_files_path/' &&
        cp '$dmjson' '$out_file'
    ]]></command>
     <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import date
{
  "data_tables":{
    "deeparg":[
      {
        "value": "deeparg_$version-#echo date.today().strftime('%d%m%Y')#",
        "name": "Files needed for running deepARG v-$version-#echo date.today().strftime('%d%m%Y')#",
        "path": "deeparg_$version",
        "db_version": "$version"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="version" type="select" label="DB version">
            <option value="@TOOL_VERSION@" selected="true">DeepARG version</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="version" value="1.0.4"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"deeparg":'/>
                    <has_text text='"db_version": "1.0.4"'/>
                    <has_text_matching expression='"value": "deeparg_1.0.4-[0-9]{8}"'/>
                    <has_text_matching expression='"name": "Files needed for running deepARG v-1.0.4-[0-9]{8}"'/>
                    <has_text text='"path": "deeparg_1.0.4"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Download data necessary for running DeepARG. It is composed of the database, scripts, metadata and models files.
    ]]></help>
    <citations>
        <citation type="doi">10.1186/s40168-018-0401-z</citation>
    </citations>
</tool>