Unify input data providing in NGS reads mappers

In the current UGENE version:

• BWA, BWA-MEM, Bowtie, Bowtie2 workflow elements have "Library" parameter with values "Single-end" and "Paired-end". When the value is "Paired-end", there are two input ports.
• TopHat has no parameter for setting SE/PE input reads. It has 4 input slots: 2 for URLs and 2 for assembly data.
• UGENE Genome Aligner also has no parameter for setting SE/PE reads. It has 2 input slots for URLs.

Ideally, there should be (like, for example, in the Trimmomatic workflow element):

• The parameter should be "Input data" with values "SE reads" and "PE reads" .
• There should be 1 input port with 1 or 2 slots for URLs depending on the value of the "Input data" parameter.

However, back compatibility should be also kept.