minillinim/MetaChecka2000 — pull request #2 by ctSkennerton (2012-11-15 14:16:35+00:00)
Title: List files on the command line

Changed the workflow so that the user can specify a list of files on the command line or a directory of fasta files. This has caused a change in the cli as there is now a new `-b` option that contains the input directory when not listing files on the command line. So the cli would change from:
```
metachecka2000 all -t -f
```

to

```
metachecka2000 all -b -t -f
```

or

```
metachecka2000 all -t -f ...
```