Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

diff data_manager/plasmidfinder_fetch_database.xml @ 0:8ad77a9dc91d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
author pimarin
date Tue, 14 Feb 2023 14:25:43 +0000
parents
children 9ef108e34063
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/plasmidfinder_fetch_database.xml	Tue Feb 14 14:25:43 2023 +0000
@@ -0,0 +1,48 @@
+<tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>plasmidfinder database builder</description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+      <![CDATA[
+        python '$__tool_directory__/plasmidfinder_fetch_database.py'
+        --db_version '$database_select'
+        '$output_file'
+      ]]></command>
+    <inputs>
+        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
+            <option value="latest" selected="true">Latest available version</option>
+            <option value="2.1">V2.1_2019-08-28</option>
+        </param>param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <!-- Test_1 DB latest -->
+        <test expect_num_outputs="1">
+            <param name="database_select" value="latest"/>
+            <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
+                <assert_contents>
+                    <has_text_matching expression='{"data_tables": {"plasmidfinder_database": [{"date": "\d\d\d\d-\d\d-\d\d", "name": "b1c9ddac0e61_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_b1c9ddac0e61_\d\d\d\d-\d\d-\d\d"' />
+                </assert_contents>
+            </output>
+        </test>
+         <!-- Test_2 DB 2.1 -->
+        <test expect_num_outputs="1">
+            <param name="database_select" value="2.1"/>
+            <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
+                <assert_contents>
+                    <has_text_matching expression='"data_tables": \{"plasmidfinder_database": \[\{"date": "\d\d\d\\d-\d\d-\d\d", "name": "2\.1_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d"' />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Download plasmidfinder database from the bitbucket repository
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
+    </citations>
+</tool>