# HG changeset patch
# User iuc
# Date 1606068168 0
# Node ID 58bcd38cecb6445bbccc790ea3be557a51f430eb
# Parent  c25855a79671c50fda57a460bf3b1636748c3272
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"

diff -r c25855a79671 -r 58bcd38cecb6 data_manager/data_manager.py
--- a/data_manager/data_manager.py	Fri Mar 27 20:34:48 2020 +0000
+++ b/data_manager/data_manager.py	Sun Nov 22 18:02:48 2020 +0000
@@ -12,7 +12,7 @@
 
 ZENODO = {
     "mitos": "2683856",
-    "mitos2": "3685310"
+    "mitos2": "4284483"
 }
 NAMES = {
     "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
@@ -71,14 +71,14 @@
     data_manager_entry['path'] = path
     data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
 
-    with open(outjson) as f:
-        params = json.loads(f.read())
+    with open(outjson) as fh:
+        params = json.load(fh)
     target_directory = params['output_data'][0]['extra_files_path']
     os.mkdir(target_directory)
     # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
     shutil.move(os.path.join(workdir, path), target_directory)
     with open(outjson, 'w') as fh:
-        fh.write(json.dumps(data_manager_json, sort_keys=True))
+        json.dump(data_manager_json, fh, sort_keys=True)
 
 
 if __name__ == '__main__':
diff -r c25855a79671 -r 58bcd38cecb6 data_manager/data_manager_mitos.xml
--- a/data_manager/data_manager_mitos.xml	Fri Mar 27 20:34:48 2020 +0000
+++ b/data_manager/data_manager_mitos.xml	Sun Nov 22 18:02:48 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1">
+<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
     <description>reference data downloader</description>
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
@@ -25,13 +25,13 @@
             </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>
+                    <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
                 </param>
             </when>
         </conditional>
@@ -47,6 +47,13 @@
             </conditional>
             <output name="out_file" file="mitos_refseq39.json"/>
         </test>
+        <test>
+            <conditional name="type_cond">
+                <param name="type_select" value="mitos2"/>
+                <param name="database" value="refseq63m"/>
+            </conditional>
+            <output name="out_file" file="mitos2_refseq63.json"/>
+        </test>
     </tests>
     <help>
 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
@@ -74,7 +81,7 @@
 - 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.
+Data is downloaded from https://zenodo.org/record/4284483.
     </help>
     <citations>
         <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
diff -r c25855a79671 -r 58bcd38cecb6 test-data/mitos2_refseq63.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mitos2_refseq63.json	Sun Nov 22 18:02:48 2020 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"mitos": {"name": "RefSeq63 Metazoa", "path": "refseq63m", "type": "mitos2", "value": "refseq63m"}}}
\ No newline at end of file