# HG changeset patch
# User bgruening
# Date 1747993723 0
# Node ID 7862ca465c6b3d694a5d518975afc7e9cfb78533

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_tax_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18

diff -r 000000000000 -r 7862ca465c6b data_manager/data_manager_sylph_tax_database.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sylph_tax_database.xml	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,60 @@
+<tool id="data_manager_sylph_tax_database" name="Download sylph-tax taxonomy metadata files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
+        <token name="@DB_VERSION@">1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">sylph-tax</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+mkdir -p '$out_file.extra_files_path'/sylph_tax_metadata_@TOOL_VERSION@ &&
+sylph-tax download --download-to '$out_file.extra_files_path'/sylph_tax_metadata_@TOOL_VERSION@ &&
+cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import date
+
+{
+    "data_tables":{
+    "sylph_tax_database":[
+    {
+        "value": "sylph_tax_downloaded_#echo date.today().strftime('%d%m%Y')#",
+        "name": "sylph tax database @TOOL_VERSION@",
+        "path": "sylph_tax_metadata_@TOOL_VERSION@",
+        "version": "@DB_VERSION@"
+    }
+    ]
+}
+        }]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="version" type="text" label="Version" value="@TOOL_VERSION@" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"sylph_tax_database":'/>
+                    <has_text_matching expression='"value": "sylph_tax_downloaded_[0-9]{8}"'/>
+                    <has_text text='"name": "sylph tax database @TOOL_VERSION@"'/>
+                    <has_text_matching expression='"path": "sylph_tax_metadata_@TOOL_VERSION@"'/>
+                    <has_text text='"version": "@DB_VERSION@"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool downloads sylph-tax taxonomy metadata files for pre-built databases.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41587-024-02412-y</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 7862ca465c6b data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_sylph_tax_database.xml" id="data_manager_sylph_tax_database">
+        <data_table name="sylph_tax_database">  <!-- Defines a Data Table to be modified. -->
+            <output> <!-- Handle the output of the Data Manager Tool -->
+                <column name="value"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="name"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">sylph_tax/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/sylph_tax/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+                <column name="version"/>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
\ No newline at end of file
diff -r 000000000000 -r 7862ca465c6b test-data/sylph_tax_database.loc.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sylph_tax_database.loc.test	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,11 @@
+#This is a tab separated file describing the location of StarAMR databases 
+#used for the StarAMR tool
+#
+#file has this format (white space characters are TAB characters)
+#
+#The columns are:
+#value	name	path    version
+#
+#For example
+#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502	ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004)	/path/to/data
+sylph_tax_downloaded_22052025	sylph tax database 1.2.0	/tmp/tmpebaga2e4/galaxy-dev/tool-data/sylph_tax/sylph_tax_metadata_1.2.0	1
diff -r 000000000000 -r 7862ca465c6b tool-data/sylph_tax_database.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sylph_tax_database.loc.sample	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,10 @@
+#This is a tab separated file describing the location of StarAMR databases 
+#used for the StarAMR tool
+#
+#file has this format (white space characters are TAB characters)
+#
+#The columns are:
+#value	name	path    version
+#
+#For example
+#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502	ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004)	/path/to/data
\ No newline at end of file
diff -r 000000000000 -r 7862ca465c6b tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="sylph_tax_database" comment_char="#">
+        <columns>value, name, path, version</columns>
+        <file path="tool-data/sylph_tax_database.loc"/>
+    </table>
+</tables>
\ No newline at end of file
diff -r 000000000000 -r 7862ca465c6b tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri May 23 09:48:43 2025 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="sylph_tax_database" comment_char="#">
+        <columns>value, name, path, version</columns>
+        <file path="${__HERE__}/test-data/sylph_tax_database.loc.test"/>
+    </table>
+</tables>
\ No newline at end of file