--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_mothur_reference_data.xml	Mon Nov 06 06:21:50 2017 -0500
@@ -0,0 +1,132 @@
+<?xml version="1.0"?>
+<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.3" tool_type="manage_data">
+    <description>Fetch and install reference data for Mothur</description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <command><![CDATA[
+        python '$__tool_directory__/fetch_mothur_reference_data.py'
+        --source=$data_source.data_source_selector
+        #if str( $data_source.data_source_selector ) == "mothur_website"
+           --datasets '${data_source.ref_data}'
+        #elif str( $data_source.data_source_selector ) == "filesystem_paths"
+           --description '${data_source.description}'
+           --paths '${data_source.paths}'
+           #if $data_source.create_symlink
+             --link
+           #end if
+        #end if
+        '${out_file}'
+    ]]></command>
+    <inputs>
+        <conditional name="data_source">
+            <param name="data_source_selector" type="select"
+                   label="Choose the source for the reference data">
+                <option value="mothur_website">Mothur website</option>
+                <option value="filesystem_paths">Filesystem paths</option>
+            </param>
+            <when value="mothur_website">
+                <param name="ref_data" type="select" display="checkboxes" multiple="true"
+                       label="Reference dataset to install">
+                    <option value="lookup_titanium">GS FLX Titanium lookup files</option>
+                    <option value="lookup_gsflx">GSFLX lookup files</option>
+                    <option value="lookup_gs20">GS20 lookup files</option>
+                    <option value="RDP_v16">RDP reference files (training set version 16)</option>
+                    <option value="RDP_v14">RDP reference files (training set version 14)</option>
+                    <option value="RDP_v10">RDP reference files (training set version 10)</option>
+                    <option value="RDP_v9">RDP reference files (training set version 9)</option>
+                    <option value="RDP_v7">RDP reference files (training set version 7)</option>
+                    <option value="RDP_v6">RDP reference files (training set version 6)</option>
+                    <option value="silva_release_128">SILVA reference files (release 128)</option>
+                    <option value="silva_release_123">SILVA reference files (release 123)</option>
+                    <option value="silva_release_119">SILVA reference files (release 119)</option>
+                    <option value="silva_release_102">SILVA reference files (release 102)</option>
+                    <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option>
+                    <option value="greengenes_May2013">Greengenes reference taxonomy and alignment v13.5 (May 2013)</option>
+                    <option value="greengenes_old">Greengenes reference taxonomy and alignment (pre-May 2013)</option>
+                    <option value="greengenes_gold_alignment">Greengenes gold alignment</option>
+                    <option value="secondary_structure_maps_silva">SILVA secondary structure maps</option>
+                    <option value="secondary_structure_maps_greengenes">Greengenes secondary structure maps</option>
+                </param>
+            </when>
+            <when value="filesystem_paths">
+                <param name="description" type="text" value="" size="50"
+                       label="Description of the data" optional="False" />
+                <param name="paths" type="text" value="" area="True" size="10x50"
+                       label="Paths to upload" optional="False"
+                       help="Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well." />
+                <param type="boolean" name="create_symlink" truevalue="create_symlink"
+                       falsevalue="copy_file"
+                       label="Create symlinks to data instead of copying into Galaxy" checked="on" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="data_sourece|ref_data" value="lookup_titanium"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="GS FLX Titanium" />
+                    <has_text text="LookUp_Titanium.pat" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+.. class:: infomark
+
+**What it does**
+
+This tool fetches reference data used by the mothur_toolsuite set of Galaxy tools,
+and populates the appropriate data tables.
+
+The reference data can be imported directly from the Mothur website, or from files
+in a server directory.
+
+Files are added to the following data tables based on file extension:
+
+ * **mothur_lookup**: for .pat files
+ * **mothur_aligndb**: for .fasta files
+ * **mothur_map**: for .map files
+ * **mothur_taxonomy**: for .tax files
+
+------
+
+**Importing from Mothur website**
+
+Reference data sets provided by the Mothur developers can be downloaded from the
+Mothur website. See the following pages to get more information about each dataset:
+
+ * Lookup data:        http://www.mothur.org/wiki/Lookup_files
+ * RDP reference data: http://www.mothur.org/wiki/RDP_reference_files
+ * Silva data:         http://www.mothur.org/wiki/Silva_reference_files
+ * Greengenes data:    http://www.mothur.org/wiki/Greengenes-formatted_databases
+ * Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map
+
+**Importing from file system paths**
+
+If reference data is already on the server filesystem then use this option to
+import it into the Mothur data tables. The appropriate data tables are determined
+based on the file extensions.
+
+Optionally a description can be added which will appear next to the base of the
+reference file name in the data table entry.
+
+------
+
+.. class:: warningmark
+
+**A note on Lane masks**
+
+Lane mask data is also available via the Mothur website (files ending in ".filter"):
+
+ * http://www.mothur.org/wiki/Lane_mask
+
+but as these data are not currently used in the toolsuite, they cannot be imported
+using this data manager.
+
+    </help>
+</tool>