Mercurial > repos > iuc > data_manager_mitos

changeset 2:19d9be08560c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
author iuc
date Sun, 22 Nov 2020 18:03:14 +0000
parents 1ff9996995ee
children 14785f8a3725
files data_manager/data_manager.py data_manager/data_manager_mitos.xml test-data/mitos2_refseq63.json
diffstat 3 files changed, 12 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager.py	Sun Nov 22 12:51:27 2020 +0000
+++ b/data_manager/data_manager.py	Sun Nov 22 18:03:14 2020 +0000
@@ -12,7 +12,7 @@
 
 ZENODO = {
     "mitos": "2683856",
-    "mitos2": "3685310"
+    "mitos2": "4284483"
 }
 NAMES = {
     "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
--- a/data_manager/data_manager_mitos.xml	Sun Nov 22 12:51:27 2020 +0000
+++ b/data_manager/data_manager_mitos.xml	Sun Nov 22 18:03:14 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mitos2_refseq63.json	Sun Nov 22 18:03:14 2020 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"mitos": {"name": "RefSeq63 Metazoa", "path": "refseq63m", "type": "mitos2", "value": "refseq63m"}}}
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