Reference/index selection for reads mapping elements

New parameter

Add a new parameter "Reference input type" to the following workflow elements:

1. "Align Reads with Bowtie"
2. "Align Reads with Bowtie2"
3. "Align Reads with BWA"
4. "Align Reads with BWA MEM"
5. "Align Reads with UGENE Genome Aligner"
6. "Find Splice Junctions with TopHat"

This should be the first parameter in the "Parameters" list in the Property Editor.
The parameter has two possible values: "Sequence" and "Index" (i.e. add a combo box).
The parameter description should be the following:

Select "Sequence" to input a reference genome as a sequence file. Note that any sequence file format, supported by UGENE, is allowed (FASTA, GenBank, etc.). The index will be generated automatically in this case.

Select "Index" to input already generated index files, specific for the tool.

Showing/hiding other parameters

Depending on the value of the new parameter show or hide other index-building parameters:

• For Bowtie:
  • Sequence: "Reference genome" parameter
  • Index: "Bowtie index folder", "Bowtie index basename"

• For Bowtie2:
  • Sequence: "Reference genome"
  • Index: "Bowtie index folder", "Bowtie index basename"
• For BWA:
  • Sequence: "Reference genome"
  • Index: "BWA index folder", "BWA index basename", "Index algorithm"
• For BWA MEM:
  • Sequence: "Reference genome"
  • Index: "BWA index folder", "BWA index basename", "Index algorithm"
• For UGENE Genome Aligner:
  • Sequence: "Reference genome"
  • Index: "Genome Aligner index folder", "Genome Aligner index basename"
• For TopHat:
  • Sequence: "Reference genome"
  • Index: "Bowtie index folder", "Bowtie index basename"

Default values and backward compatibility

The default value of the parameter for TopHat should be "Index", for other elements it should be "Sequence".
Make sure old workflows with the elements are updated, if required, and work properly.