diff data_manager/data_manager_mitos.xml @ 2:ae5ddc5a6511 draft

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

--- 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>