how to use galaxy tool interval_maf_to_merged_fasta.py

[johnfromgyh]

I want to use the stitcher to extract a given region from MAF files, stitch
it together and convert it to FASTA.

I downloaded and installed Galaxy according to the instructions from

http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the
/tools/maf directory (not clear from the paper or docs but I belive this is
the tool that implements this functionality).

How can I actually extract, stitch, convert with
interval_maf_to_merged_fasta.py?

I have difficulties figuring all necessary command line parameters out by
reading the source code.

F.e. here I tried to get the stiched FASTA conversion for a region defined
in "foo.bed" out of "chr1.maf":
python /pub1/lvyl2012/software/lyl/galaxy/tools/maf/interval_maf_to_merged_fasta.py /pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/chr1.maf -d hg17 -t cached -c 1 -s 2 -e 3 -S 6 -p hg17 -m /pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/ -z /pub1/lvyl2012/software/lyl/galaxy/tool-data/ -i /pub1/lvyl2012/ExtractMultipleAlignment/aa.bed -o /pub1/lvyl2012/ExtractMultipleAlignment/results.fa

It gives the error mssage:

The MAF source specified (/pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/) appears to be invalid



Is it necessary to index the MAF files first somehow? Do I have to set the
type of MAF file, and to what?

Would be great if someone could give a short overview how to stitch MAF
files command-line based.