Hello-,
I have had similar problems, and you can possibly solve them by using
composite datasets, which allow you to pass files to a directory whilst
having a primary file that represents the dataset (I believe Rgenetics
uses a primary HTML file containing hyperlinks to the files in the dir).
For example, in your tools command line:
script.pl $input1 $input2 $output
specifying:
script.pl $input1 $input2 $output.extra_files_dir
The extra_files_dir attribute is lets the script output files to a
directory (don't change its name). The dir can in a next step be reached
by specifying:
script2.pl $input.extra_files_dir
I am not quite in the position to explain everything, since I only use
my composite files in in-between steps yet. In other words, I don't know
how to create the primary file and let users download their composite files.
cheers,
jorrit
On 10/02/2012 05:05 PM, Sarah Maman wrote:
Bonjour,
Je souhaiterai intégrer un script perl (script quantifier de mirdeep2)
dans un nouveau tool de mon instance locale de Galaxy.
Le problème est que ce script génère plusieurs outputs (fichiers
images) mais le nombre d'outputs est variable d'une fois sur l'autre.
Il me semble que le nombre d'outputs doit être défini et fixe dans le
fichier xml du tool ? Ou existe t'il un moyen pour que le nombre
d'outputs ne soit pas précisé à l'avance ?
Merci d'avance pour votre aide,
Sarah Maman
**************
Hello,
I would like to integrate a perl script (script quantifier of
mirdeep2) in a new tool in my local instance of Galaxy.
The problem is that this script generates several outputs (image
files), but the number of outputs varies from one time to another.
It seems that the number of outputs must be defined and fixed in the
tool xml file ? Or is there a way to not specify the number of outputs ?
Thank you in advance for your help,
Sarah Maman
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