From sarah.maman@toulouse.inra.fr Tue Oct 2 11:05:56 2012 From: Sarah Maman To: galaxy-france@lists.galaxyproject.org Subject: [Galaxy-france] Gestion d'un nombre =?utf-8?q?ind=C3=A9fini?= de fichiers output / Managment of undefined outputs Date: Tue, 02 Oct 2012 17:05:46 +0200 Message-ID: <506B02CA.8000503@toulouse.inra.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2911466736489575479==" --===============2911466736489575479== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit 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 --===============2911466736489575479==-- From olivier.filangi@rennes.inra.fr Tue Oct 2 11:23:19 2012 From: Olivier Filangi To: galaxy-france@lists.galaxyproject.org Subject: Re: [Galaxy-france] Gestion d'un nombre =?utf-8?q?ind=C3=A9fini?= de fichiers output / Managment of undefined outputs Date: Tue, 02 Oct 2012 17:23:16 +0200 Message-ID: <506B06E4.6070703@rennes.inra.fr> In-Reply-To: <506B02CA.8000503@toulouse.inra.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============5355813779290070247==" --===============5355813779290070247== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Bonjour, J'ai eu =C3=A9galement ce probl=C3=A8me. J'ai choisi de cr=C3=A9er un seul fichier resultat au format HTML (donc dans = le XML du tool il y a un seul fichier output) et d'"embarquer" l'ensemble des fichiers soit sous forme d image ou de=20 fichier =C3=A0 telecharger avec un encodage base64 exemple pour un fichier texte zipp=C3=A9 :|| ||echo ''>> $html__|||||||| |echo $comments_to_down >>$html__| |echo '' >> $html__| || || |si tu ne zip pas le type mime est text/plain| || | |ou pour une image : 3D"description"' ne pas oublier d'effacer les fichiers gener=C3=A9s par l'application apr=C3= =A8s ce=20 traitement Olivier Le 02/10/2012 17:05, Sarah Maman a =C3=A9crit : > Bonjour, > > Je souhaiterai int=C3=A9grer un script perl (script quantifier de mirdeep2)= =20 > dans un nouveau tool de mon instance locale de Galaxy. > Le probl=C3=A8me est que ce script g=C3=A9n=C3=A8re plusieurs outputs (fich= iers=20 > images) mais le nombre d'outputs est variable d'une fois sur l'autre. > Il me semble que le nombre d'outputs doit =C3=AAtre d=C3=A9fini et fixe dan= s le=20 > fichier xml du tool ? Ou existe t'il un moyen pour que le nombre=20 > d'outputs ne soit pas pr=C3=A9cis=C3=A9 =C3=A0 l'avance ? > > Merci d'avance pour votre aide, > Sarah Maman > > > ************** > > Hello, > > I would like to integrate a perl script (script quantifier of=20 > mirdeep2) in a new tool in my local instance of Galaxy. > The problem is that this script generates several outputs (image=20 > 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=20 > tool xml file ? Or is there a way to not specify the number of outputs ? > > Thank you in advance for your help, > Sarah Maman > _______________________________________________ > Galaxy-France mailing list > Galaxy-France(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-france --===============5355813779290070247== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9SVNP LTg4NTktMSIKICAgICAgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIj4KICA8L2hlYWQ+CiAgPGJv ZHkgdGV4dD0iIzAwMDAwMCIgYmdjb2xvcj0iI0ZGRkZGRiI+CiAgICA8ZGl2IGNsYXNzPSJtb3ot Y2l0ZS1wcmVmaXgiPkJvbmpvdXIsPGJyPgogICAgICBKJ2FpIGV1ICZlYWN1dGU7Z2FsZW1lbnQg Y2UgcHJvYmwmZWdyYXZlO21lLiA8YnI+CiAgICAgIEonYWkgY2hvaXNpIGRlIGNyJmVhY3V0ZTtl ciB1biBzZXVsIGZpY2hpZXIgcmVzdWx0YXQgYXUgZm9ybWF0IEhUTUwgKGRvbmMKICAgICAgZGFu cyBsZSBYTUwgZHUgdG9vbCBpbCB5IGEgdW4gc2V1bCBmaWNoaWVyIG91dHB1dCk8YnI+CiAgICAg 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bGlzdHMuYngucHN1LmVkdS9saXN0aW5mby9nYWxheHktZnJhbmNlIj5odHRwOi8vbGlzdHMuYngu cHN1LmVkdS9saXN0aW5mby9nYWxheHktZnJhbmNlPC9hPgogICAgICA8YnI+CiAgICA8L2Jsb2Nr cXVvdGU+CiAgICA8YnI+CiAgICA8YnI+CiAgPC9ib2R5Pgo8L2h0bWw+Cg== --===============5355813779290070247==-- From alermine@curie.fr Tue Oct 2 11:35:17 2012 From: Alban Lermine To: galaxy-france@lists.galaxyproject.org Subject: Re: [Galaxy-france] Gestion d'un nombre =?utf-8?q?ind=C3=A9fini?= de fichiers output / Managment of undefined outputs Date: Tue, 02 Oct 2012 17:35:08 +0200 Message-ID: <506B09AC.6000003@curie.fr> In-Reply-To: <506B06E4.6070703@rennes.inra.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3338548892720302537==" --===============3338548892720302537== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Salut, Autre solution (je ne crois pas qu'il soit possible de ne pas définir les outputs à l'avance..) Créer autant de balise d'outputs qu'il peut y en avoir au max et gérer leur création avec la balise filter. (if_PNG1 == True) (if_PNG2 == True) Dans tes inputs, tu ajoutes une coche qui permet de déterminer quels outputs tu dois créer: ... Et au niveau de ta commande, tu peux jouer avec les conditions interprétées: createImage.sh #if str( $if_PNG1 ) == '1' -o $output1 #if str($if_PNG2) == '1' -o2 $output2 ... Après cette solution peut vite devenir très lourde à écrire si tu dois gérer énormément d'outputs.. ++, Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 --===============3338548892720302537==-- From alermine@curie.fr Tue Oct 2 11:42:44 2012 From: Alban Lermine To: galaxy-france@lists.galaxyproject.org Subject: Re: [Galaxy-france] Gestion d'un nombre =?utf-8?q?ind=C3=A9fini?= de fichiers output / Managment of undefined outputs Date: Tue, 02 Oct 2012 17:42:36 +0200 Message-ID: <506B0B6C.3090701@curie.fr> In-Reply-To: <506B09AC.6000003@curie.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8449044633782347466==" --===============8449044633782347466== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Re, Visite le lien suivant: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files Ils parle des différents cas de figure avec les outputs multiples: - Static Multiple Outputs - Variable Static Outputs determined by parameter values(la même méthode que celle que je t'ai décrite) - Number of Output datasets cannot be determined until tool run ++, Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 --===============8449044633782347466== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; 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boundary="===============3244650806018064227==" --===============3244650806018064227== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit 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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ --===============3244650806018064227==--