Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Peter, That's great, worked perfectly. Thank you very much, Martin On 10/02/2015 11:26 AM, Peter Cock wrote: > If you have a wrapper script, then you can do it there. > > It is also possible in the XML directly by building a composite >

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

Creating symlinks with normal extensions is a common approach here where the Galaxy filenames won't work. Peter On Fri, Oct 2, 2015 at 10:57 AM, Martin Vickers wrote: > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi all, > > I've been tasked with getting someone's R

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

If you have a wrapper script, then you can do it there. It is also possible in the XML directly by building a composite command with && separators (which must be escaped as or using CDATA), e.g. https://github.com/galaxyproject/tools-devteam/blob/master/tools/samtool_filter2/samtool_filter2.xml

[galaxy-dev] Creating R galaxy wrapper where a function checks file extension

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, I've been tasked with getting someone's R script working in our galaxy installation and I'm struggling to resolve an issue with an bioconductor function that appears to not like the galaxy naming convention (e.g. dataset_2.dat) for the bam

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Peter, Thanks for the reply. Are there any examples of this in action? Is it done in the xml wrapper somewhere or do I need to write a script that does this and then call the Rscript? Cheers, Martin On 10/02/2015 11:13 AM, Peter Cock wrote: >