Mercurial > repos > lionelguy > rnammer

annotate rnammer.xml @ 0:708bb17a1efd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial commit, rnammer.xml
author lionelguy
date Thu, 15 Aug 2013 03:29:04 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
1 <tool id="rnammer" name="rnammer" version="0.1">
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
2 <description>RNAmmer predicts 5S/8S, 16S/18S, and 23S/28S ribosomal RNA in genome sequences.</description>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
3 <requirements>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
4 <requirement type="package" version="1.2">rnammer</requirement>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
5 <requirement type="package" version="2.3.2">hmmer</requirement>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
6 </requirements>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
7 <command>rnammer -S $kingdom -m $molecules -xml $out_xml -gff $out_gff -f $out_fasta -h $out_hmm_report
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
8 #if $multi
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
9 -multi
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
10 #end if
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
11 $in_fasta
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
12 </command>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
13 <inputs>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
14 <param name="in_fasta" type="data" label="Input sequence (fasta)" help="Genome sequence" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
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">
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
16 <option value="arc">Archaea</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
17 <option value="bac" selected="true">Bacteria</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
18 <option value="euk">Eukaryotes</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
19 </param>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
20 <param name="molecules" type="select" label="Molecules" help="Which rRNAs to detect." force_select="true" multiple="true" display="checkboxes">
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
21 <option value="tsu" selected="true">TSU: 5S/8S</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
22 <option value="ssu" selected="true">SSU: 16S/18S</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
23 <option value="lsu" selected="true">LSU: 23S/28S</option>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
24 </param>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
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" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
26 </inputs>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
27 <outputs>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
28 <data name="out_xml" format="xml" label="rRNA molecules (xml)" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
29 <data name="out_gff" format="gff" label="rRNA molecules (GFF)" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
30 <data name="out_fasta" format="fasta" label="Predicted rRNA genes (fasta)" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
31 <data name="out_hmm_report" format="txt" label="HMM report" />
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
32 </outputs>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
33 <help>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
34 **What it does**
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
35
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
36 Runs rnammer, a wrapper that makes use of hmmer to identify ribosomal RNA genes on full or draft genomes.
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
37
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
38 **Citation**
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
39
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
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.
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
41
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
42 </help>
708bb17a1efd Initial commit, rnammer.xml
lionelguy
parents:
diff changeset
43 </tool>