annotate data_manager/data_manager_metaphlan_download.xml @ 6:d8dc037e3c13 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 3c1a0c4a94f78437c6df74b5348826e33e734a05

<tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">4.0.6</token>
        <token name="@VERSION_SUFFIX@">3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/>
        <exit_code range="1:" level="fatal" description="Error"/>
    </stdio>
    <command><![CDATA[
        metaphlan --install --index '$index' --bowtie2db '$out_file.extra_files_path/$index' &&
        cp '$dmjson' '$out_file'
    ]]></command>
     <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import date
{
  "data_tables":{
    "genomad":[
      {
        "dbkey": "$index",
        "value": "${index}-#echo date.today().strftime('%d%m%Y')#",
        "name": "MetaPhlAn clade-specific marker genes ($index)",
        "path": "$out_file.extra_files_path/$index",
        "db_version": #slurp
#if "SGB" in str($index)
"SGB"#slurp
#else
"legacy"#slurp
#end if
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="index" type="select" label="Version">
            <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option>
            <option value="mpa_vJun23_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202403</option>
            <option value="mpa_vJun23_CHOCOPhlAnSGB_202307" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202307</option>
            <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202212</option>
            <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">FULL: mpa_vJan21_CHOCOPhlAnSGB_202103</option>
            <option value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103">DEMO: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"db_version": "SGB"'/>
                    <has_text text='"dbkey": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"'/>
                    <has_text_matching expression='"value": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103-[0-9]{8}"'/>
                    <has_text text='"name": "MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"'/>
                    <has_text_matching expression='.*"path": ".*/mpa_vJan21_TOY_CHOCOPhlAnSGB_202103".*'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool downloads and builds the MetaPhlAn databases.
    ]]></help>
    <citations>
        <citation type="doi">1101/2020.11.19.388223</citation>
    </citations>
</tool>