Start MIRA v4 mapping wrapper; Fix tool shed URL
Rename MIRA wrapper folders
Adjust README files and TravisCI after renaming MIRA folders
Delete long deprecated fastq_filter_by_id tool

Still available as a (deprecated) entry on the Tool Shed for
reproducibility purposes:
http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_filter_by_id
Delete long deprecated sff_filter_by_id tool

Still available as a (deprecated) entry on the Tool Shed for
reproducibility purposes:
http://toolshed.g2.bx.psu.edu/view/peterjc/sff_filter_by_id
Delete long deprecated fasta_filter_by_id tool

Still available as a (deprecated) entry on the Tool Shed for
reproducibility purposes:
http://toolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id
Move fastq_paired_unpaired tool into its own folder
fastq_paired_unpaired.rst --> README.rst
Update fastq_paired_unpaired README after renames
Update TravisCI setup after fastq_paired_unpaired rename