Hi Steve, try do like this example [1]

[1]
https://github.com/leobiscassi/autodock_vina_tools/blob/dev/tools/prepare_ligand/prepare_ligand.xml

Cheers,

On Fri, Oct 21, 2016 at 2:48 PM Steve Cassidy <steve.cass...@mq.edu.au>
wrote:

> Hi,
>  I’m wrapping a tool that needs it’s input to have a known file extension
> (an audio file, eg. .wav).  Since Galaxy stores all data as .dat files the
> tool is falling over since it doesn’t know what .dat is.
>
> I thought I’d be able to get around this by hard linking the .dat file to
> the same name with a .wav extension (dataset_1.dat.wav), this works when I
> try it with the tool on the command line but within Galaxy it fails, here’s
> my <command>:
>
>         ln $signal* ${signal}.wav* &amp;
>         /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
>         BPF=$bpf INSKANTEXTGRID=$inskantextgrid
> INSORTTEXTGRID=$insorttextgrid
>         MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen
> WEIGHT=$weight
>         INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence
> OUTSYMBOL=$outsymbol
>         OUT=$output *SIGNAL=${signal}.wav*
>
> resulting in the job command line:
>
> ln /tmp/tmp7AZvx7/files/000/dataset_2.dat
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav* &
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus
> BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat
> INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10
> MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0
> NOINITIALFINALSILENCE=no OUTSYMBOL=sampa
> OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav*
>
> I’m getting an error message from the tool:
>
>
> *sox FAIL formats: can't open input file
> `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found *
> this suggests that the hard link didn’t get made.  I tried copying the
> file instead but got the same result.
>
> I could go in and patch the tool script to be more forgiving but it would
> be good to find a solution that didn’t require that if possible.
>
> Any pointers appreciated.
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
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-- 
Best regards,
*Léo Biscassi*
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