changeset 0:dd60fb1133cb draft

author simon-gladman
date Tue, 03 Sep 2013 00:24:43 -0400
children a41418a3bd38
files barrnap_wrapper.xml
diffstat 1 files changed, 55 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barrnap_wrapper.xml	Tue Sep 03 00:24:43 2013 -0400
@@ -0,0 +1,55 @@
+<tool id="barrnap" name="barrnap" version="1.0.0">
+    <description>Locate bacterial ribosomal RNA's in a fasta file. (GFF output)</description>
+    <requirements>
+        <requirement type="package" version="0.1">package_barrnap_0_1</requirement>
+    </requirements>
+    <command>
+		barrnap
+		--lencutoff $lencutoff
+		--evalue $evalue
+		$fasta_file
+		> $gff
+		2> $stderr
+    </command>
+    <inputs>
+		<param name="fasta_file" type="data" format="fasta" label="Fasta file" help="Fasta file to look for rRNA's in" />
+		<param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" />
+		<param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" />
+    </inputs>
+    <outputs>
+		<data name="stderr" format="tabular" label="${} on ${on_string}: STDERR"/>
+		<data name="gff" format="gff3" lavel="${} on ${on_string}: rRNA GFF"/>
+    </outputs>
+	<help>
+barrnap_ predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.
+This tool is designed to be a substitute for RNAmmer for bacteria. It was motivated by my desire to remove Prokka's dependency on RNAmmer which is encumbered by an free-for-academic sign-up license, and by the needed legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now.
+RNAmmer is more sophisticated than Barrnap, and more accurate. because it uses HMMER 2.x in glocal alignment mode, whereas HMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical 5/16/23S genes in bacteria, but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from RFAM, Silva, and GreenGenes.
+Barrnap is for bacteria (prokaryota) only. If you want to find rRNA genes in Archaea or Eukaryota then you should continue to use RNAmmer.
+The name Barrnap is derived from BActerial Ribosomal RNA Predictor. It was spawned at CodeFest 2013 in Berlin, Germany by Torsten Seemann and Tim Booth.
+.. _barrnap:
+**Fasta file**
+The fasta file whose contents you want to search for ribosomal RNA's.
+**Length cutoff**
+Proportional length threshold to tag a possible rRNA as pseudo.
+Similarity cutoff e-value.
+	</help>