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changeset 0:4a72de3780aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_deeparg commit 068be9bb0973bc877457d13d0d5a7c26a6cc1f96
author iuc
date Fri, 07 Feb 2025 12:17:25 +0000
parents
children 50f4ff01d845
files data_manager/data_manager_deeparg.xml data_manager_conf.xml test-data/deeparg.loc.test tool-data/deeparg.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 102 insertions(+), 0 deletions(-) [+]
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--- /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="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="version" value="1.0.4"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"deeparg":'/>
+                    <has_text text='"db_version": "1.0.4"'/>
+                    <has_text_matching expression='"value": "deeparg_1.0.4-[0-9]{8}"'/>
+                    <has_text_matching expression='"name": "Files needed for running deepARG v-1.0.4-[0-9]{8}"'/>
+                    <has_text text='"path": "deeparg_1.0.4"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download data necessary for running DeepARG. It is composed of the database, scripts, metadata and models files.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s40168-018-0401-z</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_deeparg.xml" id="data_manager_deeparg">
+        <data_table name="deeparg">  <!-- Defines a Data Table to be modified. -->
+            <output> <!-- Handle the output of the Data Manager Tool -->
+                <column name="value"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="name"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">deeparg/${value}/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/deeparg/${value}/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+                <column name="db_version"/> <!-- columns that are going to be specified by the Data Manager Tool -->
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deeparg.loc.test	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,5 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters)
+#deeparg_1.0.4	Files needed for running deepARG (1.0.4)	deeparg_1.0.4-20241010	/path/to/data	1.0.4
+deeparg_1.0.4-15012025	Files needed for running deepARG v-1.0.4-15012025	/tmp/tmpmy_tbxz7/galaxy-dev/tool-data/deeparg/deeparg_1.0.4-15012025/deeparg_1.0.4	1.0.4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/deeparg.loc.sample	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters)
+#deeparg_1.0.4	Files needed for running deepARG (1.0.4)	deeparg_1.0.4-20241010	/path/to/data	1.0.4
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="deeparg" comment_char="#">
+        <columns>value, name, path, db_version</columns>
+        <file path="tool-data/deeparg.loc.sample"/>
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Feb 07 12:17:25 2025 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="deeparg" comment_char="#">
+        <columns>value, name, path, db_version</columns>
+        <file path="${__HERE__}/test-data/deeparg.loc.test"/>
+    </table>
+</tables>