|
0
|
1 <tool id="ganon_data_manager" name="ganon data manager" version="0.0.1" tool_type="manage_data">
|
|
|
2 <description>Fetch rRNA data from NCBI RefSeq and create ganon databases</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package">python</requirement>
|
|
|
5 <requirement type="package">ganon</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
|
8 python $__tool_directory__/fetch_ganon.py --rrna $rrna --output_directory $out_dir;
|
|
|
9 ganon build -d $rrna -i *.gz;
|
|
|
10 mv $rrna.* $out_dir;
|
|
|
11 ]]></command>
|
|
|
12 <inputs>
|
|
|
13 <param argument="rrna" type="select" label="Bacterial rRNA loci" multiple="true">
|
|
|
14 <option value="5S">5S</option>
|
|
|
15 <option value="16S">16S</option>
|
|
|
16 <option value="23S">23S</option>
|
|
|
17 </param>
|
|
|
18 <param argument="out_dir" type="text" label="Output folder" value="/tool-data/ganon"/>
|
|
|
19 </inputs>
|
|
|
20 <outputs>
|
|
|
21 <data name="output_file" format="data_manager_json"/>
|
|
|
22 </outputs>
|
|
|
23 <help><![CDATA[
|
|
|
24 Retrieve RefSeq Bacterial rRNA Targeted Loci
|
|
|
25 ]]>
|
|
|
26 </help>
|
|
|
27 <citations>
|
|
|
28 </citations>
|
|
|
29 </tool>
|
