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changeset 0:4abc306ec842 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
author iuc
date Tue, 14 Jan 2025 20:27:00 +0000
parents
children 64630d815957
files data_manager/checkm2_datamanager.xml data_manager_conf.xml test-data/checkm2.loc tool-data/checkm2.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 114 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/checkm2_datamanager.xml	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,62 @@
+<tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <!-- on update run a local test setting `test` to something else than "true" -->
+        <token name="@TOOL_VERSION@">1.0.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
+    </requirements>
+    <version_command>checkm2 --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        #if $test != "true"
+            checkm2 database --download --path  '$out_file.extra_files_path'/ &&
+            mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
+        #else
+            touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
+        #end if
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+{
+  "data_tables":{
+    "checkm2":[
+      {
+        "path":"uniref100.KO.1.dmnd",
+        "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
+        "version":"@TOOL_VERSION@",
+        "value":"@TOOL_VERSION@"
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="test" type="hidden"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="test" value="true"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value":"@TOOL_VERSION@"'/>
+                    <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download and extract CheckM2 reference data.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41592-023-01940-w</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,19 @@
+<data_managers>
+    <data_manager tool_file="data_manager/checkm2_datamanager.xml" id="checkm2_build_database">
+        <data_table name="checkm2">
+            <output>
+                <column name="value"/>
+                <column name="name"/>
+                <column name="version"/>
+                <column name="path" output_ref="out_file">
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">checkm2/${value}/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/checkm2/${value}/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/checkm2.loc	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,2 @@
+
+1.0.2	CheckM2 diamond DB downloaded with version 1.0.2	1.0.2	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/checkm2.loc.sample	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,18 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a the checkm2 dabase.
+#You will need to create these data files using the following command
+
+#checkm2 database --download --path /custom/path/
+
+#and then create a checkm2_db_versioned.loc file similar to this one (store it in this
+#directory) that points to the directories in which those files are stored.
+
+#The checkm2_db_versioned.loc file has this format (longer white space
+#characters are TAB characters):
+#
+#<unique_build_id>	<display_name>	<version>	<file_base_path>
+
+#The <version> column indicates the checkm2 version that generated the database
+
+#
+#diamond_db_1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, version, path</columns>
+        <file path="tool-data/checkm2.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of rnastar indexes for testing -->
+    <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, version, path</columns>
+        <file path="${__HERE__}/test-data/checkm2.loc" />
+    </table>
+</tables>
\ No newline at end of file