changeset 0:5c31cd602239 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/iphop_datamanager.xml	Mon Oct 14 14:56:29 2024 +0000
@@ -0,0 +1,61 @@
+<tool id="iphop_build_database" name="iPHoP" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.3.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">22.01</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">iphop</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir db &&
+        iphop download
+            --db_dir db/
+            --db_version $db_version
+            ## --full_verify  https://bitbucket.org/srouxjgi/iphop/issues/114/db-download-verification-error
+            --no_prompt &&
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+{
+  "data_tables":{
+    "checkv":[
+      {
+        "path":"db",
+        "name":"Version $db_version",
+        "version":"$db_version",
+        "value":"$db_version"
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="db_version" type="select" multiple="false" label="Database Version">
+            <option value="iPHoP_db_Aug23_rw">iPHoP_db_Aug23_rw</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <!-- <test expect_num_outputs="1">
+            <param name="db_version" value="iPHoP_db_Aug23_rw" />
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value":"iPHoP_db_Aug23_rw"'/>
+                    <has_text text='"name":"Version iPHoP_db_Aug23_rw"'/>
+                </assert_contents>
+            </output>
+        </test> -->
+    </tests>
+    <help><![CDATA[
+Download and extract iPHoP reference data
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pbio.3002083</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Mon Oct 14 14:56:29 2024 +0000
@@ -0,0 +1,19 @@
+<data_managers>
+    <data_manager tool_file="data_manager/iphop_datamanager.xml" id="iphop_build_database">
+        <data_table name="iphop">
+            <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}">iphop/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/iphop/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/iphop.loc.sample	Mon Oct 14 14:56:29 2024 +0000
@@ -0,0 +1,2 @@
+# Format:
+# value	name	version	path
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Oct 14 14:56:29 2024 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- iphop reference data  -->
+    <table name="iphop" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="tool-data/iphop.loc" />
+    </table>
+</tables>