Mercurial > repos > ufz > genomad_build_database

changeset 3:34b729713d0c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_genomad commit fea5692fe5258a520e43b739c5aa4d109756123f
author ufz
date Fri, 13 Jun 2025 20:40:26 +0000
parents 75abfb03b635
children
files data_manager/genomad_datamanager.xml
diffstat 1 files changed, 12 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/genomad_datamanager.xml	Wed Dec 18 12:30:30 2024 +0000
+++ b/data_manager/genomad_datamanager.xml	Fri Jun 13 20:40:26 2025 +0000
@@ -2,8 +2,8 @@
 <tool id="genomad_build_database" name="geNomad" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>database builder</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.8.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">1.11.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@PROFILE@">22.01</token>
     </macros>
     <requirements>
@@ -15,7 +15,8 @@
             ## #if $version == "test"
             ##     https://zenodo.org/records/11945948/files/genomad_microdb.tar.gz?download=1
             ## #else
-                https://zenodo.org/records/10594875/files/genomad_db_v${version}.tar.gz?download=1
+                https://portal.nersc.gov/genomad/__data__/genomad_db_v${version}.tar.gz
+                ## alternatively https://zenodo.org/records/14886553, but constructing the links is more complicated
             ## #end if
         | tar -xzv &&
         mkdir -p '$out_file.extra_files_path' &&
@@ -38,8 +39,9 @@
         </configfile>
     </configfiles>
     <inputs>
-        <param name="version" type="select" multiple="false" label="Database Version" help="Download the chosen version from https://zenodo.org/records/10594875">
+        <param name="version" type="select" multiple="false" label="Database Version" help="Download the chosen version from https://portal.nersc.gov/genomad/__data__/">
             <option value="1.7">1.7</option>
+            <option value="1.9">1.9</option>
             <!-- <option value="test">test</option> -->
         </param>
     </inputs>
@@ -48,17 +50,19 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="version" value="1.7" />
+            <param name="version" value="1.9" />
             <output name="out_file">
                 <assert_contents>
-                    <has_text text='"value":"1.7"'/>
-                    <has_text text='"name":"Version 1.7"'/>
+                    <has_text text='"value":"1.9"'/>
+                    <has_text text='"name":"Version 1.9"'/>
                 </assert_contents>
             </output>
         </test>
     </tests>
     <help><![CDATA[
-Download and extract geNomad database from https://zenodo.org/records/10594875
+Download and extract geNomad database from https://portal.nersc.gov/genomad/__data__/
+
+Check for tool and DB version compatibility here: https://portal.nersc.gov/genomad/__data__/releases.txt
     ]]></help>
     <citations>
         <citation type="doi">10.1186/gb-2014-15-3-r46</citation>