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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