--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_db.xml	Thu Apr 25 13:47:16 2019 -0400
@@ -0,0 +1,73 @@
+<tool id="metaquantome_db" name="metaQuantome: database" version="@GVERSION@">
+    <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>