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Initial commit, rnammer.xml
author lionelguy
date Thu, 15 Aug 2013 03:29:04 -0400
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1 <tool id="rnammer" name="rnammer" version="0.1">
2 <description>RNAmmer predicts 5S/8S, 16S/18S, and 23S/28S ribosomal RNA in genome sequences.</description>
3 <requirements>
4 <requirement type="package" version="1.2">rnammer</requirement>
5 <requirement type="package" version="2.3.2">hmmer</requirement>
6 </requirements>
7 <command>rnammer -S $kingdom -m $molecules -xml $out_xml -gff $out_gff -f $out_fasta -h $out_hmm_report
8 #if $multi
9 -multi
10 #end if
11 $in_fasta
12 </command>
13 <inputs>
14 <param name="in_fasta" type="data" label="Input sequence (fasta)" help="Genome sequence" />
15 <param name="kingdom" type="select" label="Domain" help="Which domain of Life does your sequence belong to." force_select="true" multiple="false" display="radio">
16 <option value="arc">Archaea</option>
17 <option value="bac" selected="true">Bacteria</option>
18 <option value="euk">Eukaryotes</option>
19 </param>
20 <param name="molecules" type="select" label="Molecules" help="Which rRNAs to detect." force_select="true" multiple="true" display="checkboxes">
21 <option value="tsu" selected="true">TSU: 5S/8S</option>
22 <option value="ssu" selected="true">SSU: 16S/18S</option>
23 <option value="lsu" selected="true">LSU: 23S/28S</option>
24 </param>
25 <param name="multi" type="boolean" label="Run in parallel?" help="Runs all molecules and both strands in parallel. Require 6 threads." truevalue="true" falsevalue="false" checked="true" />
26 </inputs>
27 <outputs>
28 <data name="out_xml" format="xml" label="rRNA molecules (xml)" />
29 <data name="out_gff" format="gff" label="rRNA molecules (GFF)" />
30 <data name="out_fasta" format="fasta" label="Predicted rRNA genes (fasta)" />
31 <data name="out_hmm_report" format="txt" label="HMM report" />
32 </outputs>
33 <help>
34 **What it does**
35
36 Runs rnammer, a wrapper that makes use of hmmer to identify ribosomal RNA genes on full or draft genomes.
37
38 **Citation**
39
40 Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007 Apr 22.
41
42 </help>
43 </tool>