diff data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml @ 0:36ba79e745fd draft

Uploaded
author estrain
date Mon, 23 May 2022 02:20:25 +0000
parents
children 650186ccc063
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml	Mon May 23 02:20:25 2022 +0000
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+<tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="0.0.3" profile="20.01">
+    <requirements>
+        <requirement type="package">blast</requirement>
+        <requirement type="package">hmmer</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/data_manager_amrfinderplus.py --name $amrdbname --out ${output_file};
+    ]]></command>
+    <inputs>
+      <param name="amrdbname" type="text" label="Name of AMRFinderPlus database"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+    </help>
+    <citations>
+     Refer to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ for latest database version number.
+    </citations>
+</tool>