--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_mitos.xml	Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,86 @@
+<?xml version="1.0"?>
+<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1">
+    <description>reference data downloader</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    python '$__tool_directory__/data_manager.py' 
+    --out '${out_file}'
+    --type '$type_cond.type_select'
+    --db '$type_cond.database'
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="type_cond">
+            <param name="type_select" type="select" label="MITOS version">
+                <option value="mitos">MITOS</option>
+                <option value="mitos2">MITOS2</option>
+            </param>
+            <when value="mitos">
+                <param name="database" type="select" label="Reference data version">
+                    <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
+                </param>
+            </when>
+            <when value="mitos2">
+                <param name="database" type="select" label="Reference data version">
+                    <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
+                    <option value="refseq63m">RefSeq63 Metazoa</option>
+                    <option value="refseq63f">RefSeq63 Fungi</option>
+                    <option value="refseq63o">RefSeq63 Opisthokonta</option>
+                    <option value="refseq89m">RefSeq89 Metazoa</option>
+                    <option value="refseq89f">RefSeq89 Fungi</option>
+                    <option value="refseq89o">RefSeq89 Opisthokonta</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="type_cond">
+                <param name="type_select" value="mitos"/>
+                <param name="database" value="mitos1-refdata"/>
+            </conditional>
+            <output name="out_file" file="mitos_refseq39.json"/>
+        </test>
+    </tests>
+    <help>
+This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
+
+For MITOS the reference data includes 
+
+- protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
+- covariance models for tRNAs and rRNAs as described in Jühling et al 2012
+
+Data is downloaded from https://zenodo.org/record/2683856.
+
+For MITOS2 the reference data sets are available for three different taxons
+
+- Metazoa
+- Fungi
+- Opisthokonta
+
+these have been computed for RefSeq release 63 and 89. In addition the reference data 
+for MITOS1 has been converted to be usable in MITOS2.
+contains
+
+The reference data sets contain: 
+
+- protein data bases derived from the corresponding RefSeq release Donath et al. 2019
+- covariance models computed for the data in the RefSeq releas based on the MITOS1 models 
+- in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
+
+Data is downloaded from https://zenodo.org/record/3685310.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
+        <citation type="doi">10.1093/nar/gkr1131</citation>
+        <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
+        <citation type="doi">10.1093/nar/gkz833</citation>
+    </citations>
+</tool>
+