Made modifications to scripts, merged library functions into single work...

...flow file per discussion with Greg C. Should cover automation of commands for multiple input fastq files for join_paired_ends.py, extract_barcodes.py, and split_libraries_fastq.py. Putting all of these under #1715 as they are related code/functionality. The script names were changed to "multiple_" + joined_paired_ends, split_libraries_fastq and extract_barcodes as they now will use the workflow code to directly call the commands rather than just generating the commands.
This needs to be the output of ``parse_qiime_parameters(parameter_f)``.