diff data_manager/ganon_data_manager.xml @ 0:a50614a513f3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/ganon_data_manager.xml	Thu Jul 04 21:42:31 2019 -0400
@@ -0,0 +1,29 @@
+<tool id="ganon_data_manager" name="ganon data manager" version="0.0.1" tool_type="manage_data">
+    <description>Fetch rRNA data from NCBI RefSeq and create ganon databases</description>
+    <requirements>
+        <requirement type="package">python</requirement>
+        <requirement type="package">ganon</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+       python $__tool_directory__/fetch_ganon.py --rrna $rrna --output_directory $out_dir; 
+       ganon build -d $rrna -i *.gz;
+       mv $rrna.* $out_dir;
+    ]]></command>
+    <inputs>
+        <param argument="rrna" type="select" label="Bacterial rRNA loci" multiple="true">
+          <option value="5S">5S</option>
+          <option value="16S">16S</option>
+          <option value="23S">23S</option>
+        </param>
+        <param argument="out_dir" type="text" label="Output folder" value="/tool-data/ganon"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <help><![CDATA[
+    Retrieve RefSeq Bacterial rRNA Targeted Loci
+    ]]>
+    </help>
+    <citations>
+    </citations>
+</tool>