Hi David, tha BAM file is compressed in the BGZF format and is not uncompressed by default. So I would try the following:
- write your own datatype http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes - write a sniffer similar to the BAM sniffer https://bitbucket.org/galaxy/galaxy-central/src/8fc56b85e0a5353ffd6790685a4a7d8a84938409/lib/galaxy/datatypes/binary.py Thanks to the wonderful toolshed it is also possible to include datatypes in your repo. http://wiki.galaxyproject.org/ToolShedDatatypesFeatures Hopefully that will work out! Bjoern > Hello, > > I have a tool that needs a directory containing a bunch of files as an > input : mytool -d $directory -p param1 -o $output ... > > I thought the best approach would be to use a Zip file that I would > temporally uncompress in a bash wrapper. > But when I upload the zip file, galaxy unzip it. > > What would you recommend to accomplish such a task ? I want that tool > to be installable from a toolshed, so I don't want to modify the > upload.py script or any other files. > > Thanks, > > David > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
