changeset 2:ae5ddc5a6511 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit b63133897598f2881de7bad1f18fcd69d7d7e9df-dirty"

Binary file data_manager/.data_manager_mitos.xml.swp has changed

--- a/data_manager/data_manager.py	Sat Mar 21 15:32:06 2020 +0000
+++ b/data_manager/data_manager.py	Wed Dec 15 11:01:00 2021 +0000
@@ -12,7 +12,7 @@
 
 ZENODO = {
     "mitos": "2683856",
-    "mitos2": "3685310"
+    "mitos2": "4284483"
 }
 NAMES = {
     "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
@@ -53,11 +53,10 @@
         if src:
             src.close()
     with tarfile.open(tarfname, "r:bz2") as tar:
+        dirname = tar.getnames()[0]
         tar.extractall(workdir)
     os.remove(tarfname)
-    unzipped = os.listdir(workdir)
-    assert len(unzipped) == 1
-    return unzipped[0]
+    return dirname
 
 
 def main(tpe, db, outjson):
@@ -72,13 +71,14 @@
     data_manager_entry['path'] = path
     data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
 
-    params = json.loads(open(outjson).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))
+        json.dump(data_manager_json, fh, sort_keys=True)
 
 
 if __name__ == '__main__':

--- a/data_manager/data_manager_mitos.xml	Sat Mar 21 15:32:06 2020 +0000
+++ b/data_manager/data_manager_mitos.xml	Wed Dec 15 11:01:00 2021 +0000
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
-    <description>reference data downloader</description>
+    <description>reference data downloader blah</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
     python '$__tool_directory__/data_manager.py' 
@@ -22,13 +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>
@@ -44,6 +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.
@@ -53,6 +63,8 @@
 - 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
@@ -68,6 +80,8 @@
 - 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/4284483.
     </help>
     <citations>
         <citation type="doi">10.1016/j.ympev.2012.08.023</citation>

--- a/data_manager_conf.xml	Sat Mar 21 15:32:06 2020 +0000
+++ b/data_manager_conf.xml	Wed Dec 15 11:01:00 2021 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/data_manager_mitos.xml" id="mitos_fetcher" version="0.0.2">
+    <data_manager tool_file="data_manager/data_manager_mitos.xml" id="mitos_fetcher" version="0.0.1">
         <data_table name="mitos">
             <output>
                 <column name="value" />

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mitos2_refseq63.json	Wed Dec 15 11:01:00 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"mitos": {"name": "RefSeq63 Metazoa", "path": "refseq63m", "type": "mitos2", "value": "refseq63m"}}}
\ No newline at end of file

--- a/test-data/mitos_refseq39.json	Sat Mar 21 15:32:06 2020 +0000
+++ b/test-data/mitos_refseq39.json	Wed Dec 15 11:01:00 2021 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"mitos": {"path": "mitos1-refdata", "type": "mitos", "name": "RefSeq39 + MiTFi tRNA models", "value": "mitos1-refdata"}}}
\ No newline at end of file
+{"data_tables": {"mitos": {"name": "RefSeq39 + MiTFi tRNA models", "path": "mitos1-refdata", "type": "mitos", "value": "mitos1-refdata"}}}
\ No newline at end of file