annotate data_manager/ncbi_taxonomy_fetcher.xml @ 8:2649aece3781 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_fetch_ncbi_taxonomy commit cf8607692417bdc4f663c726aea34c1056dd9c48

<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.1" profile="24.0">
    <description>taxonomy downloader</description>
    <requirements>
        <requirement type="package" version="1.25.0">wget</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        set -o pipefail;

        mkdir -p '$out_file.extra_files_path/taxonomy/' &&
        wget -O - '$taxonomy_url' | tar -xz -C '$out_file.extra_files_path/taxonomy/' &&
        if [[ ! -f '$out_file.extra_files_path/taxonomy/nodes.dmp' ]]; then >&2 echo "nodes.dmp missing"; exit 1; fi &&

        #if $name_maps
            mkdir -p '$out_file.extra_files_path/accession2taxid/' &&
            #if $partial_data
                #set files = ['pdb.accession2taxid']
            #else
                #set files = ['dead_nucl.accession2taxid', 'dead_prot.accession2taxid', 'dead_wgs.accession2taxid', 'nucl_gb.accession2taxid', 'nucl_wgs.accession2taxid', 'pdb.accession2taxid', 'prot.accession2taxid', 'prot.accession2taxid.FULL']
            #end if
            #for file in files
                wget -O - ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/${file}.gz | gunzip -c > '$out_file.extra_files_path/accession2taxid/${file}' &&
            #end for
        #end if
        cp '$dmjson' '$out_file'
    ]]>
    </command>
        <configfiles>
        <configfile name="dmjson"><![CDATA[#slurp
#if $database_name == ""
    #import datetime
    #import os.path
    #set now = datetime.datetime.now().strftime("%Y-%m-%d-%H%M%S")
    #set basename = os.path.basename(str($taxonomy_url))[:-7]
    #set value = basename + "_" + now
    #set name = basename + " " + now
#else
    #set value = $database_name.lower()
    #set name = $database_name
#end if
{
  "data_tables":{
    "ncbi_taxonomy":[
      {
        "value": "$value",
        "name": "$name",
        "path": "."
      }
    ]
#if $name_maps
    ,"ncbi_accession2taxid":[
      {
        "value": "$value",
        "name": "$name",
        "path": "."
      }
    ]
#end if
  }
}]]></configfile>
    </configfiles>
    <inputs>
        <param name="database_name" type="text" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
        <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
        <param name="name_maps" type="boolean" label="Also download accession2taxid data" checked="false" />
        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="database_name" value="tax_name"/>
            <output name="out_file" value="taxonomy.json"/>
        </test>
        <test>
            <output name="out_file">
                <assert_contents>
                    <has_text_matching expression='"value": "taxdump_\d\d\d\d-\d\d-\d\d-\d\d\d\d\d\d"'/>
                    <has_text_matching expression='"name": "taxdump \d\d\d\d-\d\d-\d\d-\d\d\d\d\d\d"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="database_name" value="tax_name"/>
            <param name="name_maps" value="true"/>
            <param name="partial_data" value="--partial"/>
            <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
        </test>
    </tests>
    <help>
        Download a taxonomy dump from a provided URL.
        The default URL is the latest dump from NCBI taxonomy.
        The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021).
    </help>
</tool>