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.

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