Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

diff data_manager/fetch_artic_primers.xml @ 19:d118e256faca draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
author sanbi-uwc
date Thu, 16 Apr 2020 10:19:57 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_artic_primers.xml	Thu Apr 16 10:19:57 2020 +0000
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+<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.1" tool_type="manage_data" profile="19.05">
+    <requirements>
+        <requirement type="package">python</requirement>
+        <requirement type="package" version="2.22.0">requests</requirement>
+    </requirements>
+    <!-- fetch all the primers in one go -->
+    <command detect_errors="exit_code">
+    python '$__tool_directory__/fetch_artic_primers.py'
+        --galaxy_datamanager_filename '${output_file}'
+    </command>
+    <inputs>
+        <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
+            <option value="ARTICv1" selected="true">ARTIC v1</option>
+            <option value="ARTICv2" selected="true">ARTIC v2</option>
+            <option value="ARTICv3" selected="true">ARTIC v3</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="ARTIC"/>
+                </assert_contents>
+            </output>        
+        </test>
+    </tests>
+</tool>
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