# HG changeset patch
# User ufz
# Date 1726480374 0
# Node ID 200343b50d4615f815427e07b58ad57b0ef12207

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_vibrant commit 652d6d214d2de01b29badbb1fad8648d6fd6153b

diff -r 000000000000 -r 200343b50d46 data_manager/vibrant_datamanager.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vibrant_datamanager.xml	Mon Sep 16 09:52:54 2024 +0000
@@ -0,0 +1,55 @@
+<tool id="vibrant_build_database" name="vibrant" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.2.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">22.01</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">VIBRANT</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">vibrant</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        set -eo pipefail; 
+        download-db.sh vibrant_db &&
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+{
+  "data_tables":{
+    "vibrant":[
+      {
+        "path":"vibrant_db",
+        "name":"Version @TOOL_VERSION@",
+        "version":"@TOOL_VERSION@",
+        "value":"@TOOL_VERSION@"
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs/>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <!-- <test expect_num_outputs="1">
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value":"@TOOL_VERSION@"'/>
+                    <has_text text='"name":"Version @TOOL_VERSION@"'/>
+                </assert_contents>
+            </output>
+        </test> -->
+    </tests>
+    <help><![CDATA[
+Download and vibrant reference data using https://raw.githubusercontent.com/AnantharamanLab/VIBRANT/master/databases/VIBRANT_setup.py
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s40168-020-00867-0</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 200343b50d46 data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Mon Sep 16 09:52:54 2024 +0000
@@ -0,0 +1,19 @@
+<data_managers>
+    <data_manager tool_file="data_manager/vibrant_datamanager.xml" id="vibrant_build_database">
+        <data_table name="vibrant">
+            <output>
+                <column name="value"/>
+                <column name="name"/>
+                <column name="version"/>
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">vibrant_databases/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/vibrant_databases/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
diff -r 000000000000 -r 200343b50d46 tool-data/vibrant.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vibrant.loc.sample	Mon Sep 16 09:52:54 2024 +0000
@@ -0,0 +1,7 @@
+# data for vibrant can be downloaded using download-db.sh
+# - value needs to be a unique identifier (maybe date)
+# - name what is shown to the user
+# - version store the vibrant version
+# - path
+# Format:
+# value	name	version	path
\ No newline at end of file
diff -r 000000000000 -r 200343b50d46 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Sep 16 09:52:54 2024 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- vibrant reference data  -->
+    <table name="vibrant" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="tool-data/vibrant.loc" />
+    </table>
+</tables>