<tool id="cat_prepare" name="CAT prepare" version="@VERSION@.0">
    <description>a database for CAT - Contig Annotation Tool</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #import os.path
        #set $catdb = $cat_db.files_path
        mkdir -p $catdb &&
        echo CAT_DB `date '+%Y-%m-%d'` "@DATABASE_FOLDER@" "@TAXONOMY_FOLDER@" > $cat_db &&
        CAT prepare --fresh
        --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
        --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
    ]]></command>
    <inputs>
    </inputs>
    <outputs>
        <data name="cat_db" format="txt" />
    </outputs>
    <help><![CDATA[
**CAT prepare**

Prepare CAT reference data for classifying metagomic contigs or genome assemblies.

**NOTE:** This requires over a 100GB of RAM, 250GB of disk space, and up to 24 hours.

@COMMON_HELP@
    ]]></help>
    <expand macro="citations" />
</tool>