fix management of bowtie indexes and update help of the tool to reflect the use of fastq or fasta input files
fix management of bowtie indexes and update help of the tool to reflect the use of fastq or fasta input files

chamaelj/tools-artbio,ARTbio/tools-artbio,drosofff/tools-artbio,chamaelj/tools-artbio,chamaelj/tools-artbio,drosofff/tools-artbio,drosofff/tools-artbio,ARTbio/tools-artbio,drosofff/tools-artbio,ARTbio/tools-artbio,ARTbio/tools-artbio