diff data_manager/data_manager_deeparg.xml @ 0:4a72de3780aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_deeparg commit 068be9bb0973bc877457d13d0d5a7c26a6cc1f96

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_deeparg.xml	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,60 @@
+<tool id="data_manager_deeparg" name="Download data for DeepARG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.4</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">deeparg</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        deeparg download_data -o '$out_file.extra_files_path/' &&
+        cp '$dmjson' '$out_file'
+    ]]></command>
+     <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import date
+{
+  "data_tables":{
+    "deeparg":[
+      {
+        "value": "deeparg_$version-#echo date.today().strftime('%d%m%Y')#",
+        "name": "Files needed for running deepARG v-$version-#echo date.today().strftime('%d%m%Y')#",
+        "path": "deeparg_$version",
+        "db_version": "$version"
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="version" type="select" label="DB version">
+            <option value="@TOOL_VERSION@" selected="true">DeepARG version</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="version" value="1.0.4"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"deeparg":'/>
+                    <has_text text='"db_version": "1.0.4"'/>
+                    <has_text_matching expression='"value": "deeparg_1.0.4-[0-9]{8}"'/>
+                    <has_text_matching expression='"name": "Files needed for running deepARG v-1.0.4-[0-9]{8}"'/>
+                    <has_text text='"path": "deeparg_1.0.4"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download data necessary for running DeepARG. It is composed of the database, scripts, metadata and models files.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s40168-018-0401-z</citation>
+    </citations>
+</tool>