Thanks for the answer,

so I tryed to write a wrapper, but the main script is not recognize.
When I'm calling my wrapper in the xml file, I don't have to specify
the full path but then from my wrapper if I want to call my main script
I can't if this one is not on the PATH ? the wrapper current directory
is the job_working_directory, there is anyway to access my main script
just like it's done for the wrapper ?

thanks for your answer,
Jerome





Peter Cock a écrit :
On Mon, Jun 6, 2011 at 2:45 PM, Mariette <jmari...@toulouse.inra.fr> wrote:
Hi everyone,

I'm new in galaxy and I want to create a component, so I have multiple
questions.
The component executes a script which takes different formats :
fasta|fastq|sff. As output it takes a folder, to do so I used the
extra_files_path attribute of an output data
(--out='$output.extra_files_path'). The result file is stored in this folder
with the log file and should be in the same format as the input one.
I wrote the xml file and it works just fine, however as it's a folder there
is no way to use the result file(s) for further analysis. How can I manage
this ?

I use a wrapper script which moves the output file from the sub-directory
to the location Galaxy requested.

Regarding the file format, if you only have one input file you can use
format="input", otherwise use the change_format tag in the XML.

Also it can happen that there is more than 1 file outputted, how can I
manage multiple outputs ?

An other question about the input format, I have an option to the script to
specify the format. I saw there is auto-format detection routines in galaxy,
there is a way so I can call them to automatically complete this option ?

Normally the wrapper specifies the output format explicitly.

Peter
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