| The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
This wrapper works with RiboPicker 0.4.3 with the following patch: --- ribopicker-standalone-0.4.3/ribopicker.pl 2011-12-01 18:06:44.000000000 -0500 +++ ../0.4.3/bin/ribopicker_galaxy.pl 2012-10-16 18:32:03.512372941 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl #=============================================================================== # Author: Robert SCHMIEDER, Computational Science Research Center @ SDSU, CA @@ -422,10 +422,12 @@ Xcount = 3X Xfasta = Xfastq = Xqual = 0X Xformat = 'unknown'X - - open(FILE,"perl -p -e 's/Xr/Xn/gXs/XnXn/Xn/g' < Xfile X") or die "ERROR: Could not open file Xfile: X! Xn"X + open(FILE,'<', Xfile) or die "ERROR: Could not open file Xfile: X! Xn"X while (<FILE>) { chomp()X + s/^Xs+//gX next unless(length(X_))X if(Xcount-- == 0) { lastX |
hg clone https://toolshed.g2.bx.psu.edu/repos/malex/ribopicker
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Easy identification and removal of rRNA-like sequences. | 1.0.0 | any | |