comparison tRNAscan.py @ 3:f4416f1a674a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44

2:6d97da269ee2

import sys
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import subprocess


def main(args):
    """
        Call from galaxy:
        tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output

            tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $tabular_output $inputfile;
    """
    cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] )
    child = subprocess.Popen(cmd.split(),
        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    stdout, stderr = child.communicate()

3:f4416f1a674a

import sys
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import subprocess

def main(args):
    """
        Call from galaxy:
        tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output

            tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -Q -y -q -b -o $tabular_output $inputfile;
    """
    cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] )
    child = subprocess.Popen(cmd.split(),
        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    stdout, stderr = child.communicate()