<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>download the GO, EC, and NCBI databases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p data &&
        #set $database_list = str($databases).split(',')
        #for $d in $database_list
          metaquantome db '$d'
          --dir data &&
        #end for
        tar --create --file '$outfile' data
    ]]></command>
    <inputs>
        <param name="databases" type="select" multiple="True" display="checkboxes"
          label="Databases to Download">
          <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
          <option value="go" selected="true">Gene Ontology Database</option>
          <option value="ec" selected="true">Enzyme Commission (EC) database</option>
        </param>
    </inputs>
    <outputs>
        <data format="tar" name="outfile" label="metaquantome databases"/>
    </outputs>
    <tests>
      <test>
        <param name="databases" value="go"/>
        <output name="outfile">
          <assert_contents>
            <has_text text="ontology: go"/>
            <has_text text="ontology: go/subsets/goslim_metagenomics"/>
          </assert_contents>
        </output>
      </test>
    </tests>
    <help>
<![CDATA[
metaQuantome database
=====================

metaQuantome uses freely available bioinformatic databases to expand your set of direct annotations.
For most cases, all 3 databases can be downloaded (the default).

The databases are:

1. NCBI taxonomy database. This contains a list of all currently identified taxa and the
relationships between them.

2. Gene Ontology (GO) term database. metaQuantome uses the OBO format of the database. Specifically, two
files are used: the go-basic.obo file, which is a simplified version of the GO database that is guaranteed to be acyclic,
and the metagenomics slim GO, which is a subset of the full GO that is useful for microbiome research. More details are available at
http://geneontology.org/docs/download-ontology/

3. ENZYME database with Enzyme Classification (EC) numbers. This database classifies enzymes and organizes the
relationships between them.

This module downloads the most recent releases of the specified databases and stores them in a single file, which can then
be accessed by the rest of the metaQuantome modules.  For reference,
the taxonomy database is the largest (~500 Mb), while the GO and EC databases are smaller: ~34 Mb and ~10Mb, respectively.

Also, note that the databases will be stored in the history so that the date of download can be referenced later.
Thus, the databases will not be modified, except for the NCBI database, which is updated every time ``metaQuantome: expand`` is run (this
is a limitation of the Python package ete3, used within metaQuantome).

Questions, Comments, Problems, Kudos
------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
]]></help>
    <expand macro="citations" />
</tool>