Unify specifying of output files in NGS reads mappers

In the current UGENE version:

• BWA, BWA-MEM, Bowtie, Bowtie2, UGENE Genome Aligner workflow elements have "Output folder" and "Output file name" parameters.
• TopHat has "Output folder" parameter (it outputs 4 files, the BAM file always have name "accepted_hits.bam").

Furthermore, the "Output folder" parameter is empty by default and the order of the parameters in the Property Editor differs for different workflow elements.

It is required to modify the elements as follows

• Leave only "Output file" parameter.
• Make it the last parameter for the element in the Property Editor.
• Use the "Auto" value (like in Trimmomatic).

Make sure correct names are generated in both cases:

• when SE reads have been input
• when PE reads have been input

Back compatibility should be also kept.