Add an option to give various Pathway Tools option to mpwt.

[ArnaudBelcour]

At this moment if you give an option to mpwt (like pathway prediction score, pathway Hole Filler), they will be applied to all the runs of the input folder.

It could be interesting to add a new option to give a file that can give different options (like different pathway prediction score) to the different run when using mpwt.

[ArnaudBelcour]

After thinking about it, it seems not possible as the pathway prediction score is written in the ptools-init file. So only one pathway prediction score can be written at a time during a run of mpwt.

One way to do this could be to launch a bunch of Pathway Tools processes according to a pathway prediction score, wait there end and then launch another bunch of processes with different pathway prediction score. This could be possible but could need more work so I think it will not made it into the 0.7.0.