On Fri, Jun 8, 2012 at 9:15 AM, Nicholas Robinson
<nicholas.robin...@nofima.no> wrote:
> Hi,
> 1. INPUT
> I am trying to make a simple tool that sends a command to run crimap without
> a wrapper ie.
> .............
> <command>
> crimap $param_file  $option  &gt;$output1
> </command>
> ..............
> However, crimap expects a .par file as input (ie. $param_file should be a
> .par file). Because of this I get the error:
> ERROR: Parameter file
> '/home/galaxy/galaxy-dist/database/job_working_directory/001/1434/tmpe5hErw'
> does not have '.par' suffix
> ...
> Is there a simple way around this (using more lines in the command)?

You could try something like this (untested):

ln -s $param_file $param_file.par;
crimap $param_file  $option  &gt;$output1

The idea here is to tell Galaxy to issue two commands, the first a shell
call to create a symlink with the desired extension pointing at the input
filename from Galaxy. i.e. If $param_file was /path/to/file/dataset_123.dat
you'd make a symlink /path/to/file/dataset_123.dat.par - but check if you
need to remove the symlink afterwards.

Anything more that that and I would use a wrapper script in whatever
you are most comfortable with (e.g. shell, Perl, or Python). e.g.

my_script $param_file $option $output1

where the my_script file is marked executable with a hashbang
(or set the interpreter in the command tag), and the script could
be just:

ln -s $param_file $param_file.par
crimap $param_file  $option > $output1
rm $param_file.par


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