Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
If anyone was wondering, I ended up sending the name of the repeat to the function in the code file which is a list of dictionaries and in the dictionaries you have an index and the other parameters in the repeat so as long as you know the name of the parameters you are golden. On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > > > On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu < > katherine.beaulieu...@gmail.com> wrote: > >> Hi Bjorn, >> Thank you for taking the time to reply to my question. I don't think this >> quite fits what I am trying to accomplish. I am trying to pass a set of >> metadata key value pairs, where the user can have as many key value pairs >> as they want, generated with a repeat parameter. I would need to pass the >> entire contents of the repeat parameter to the code file to generate a >> dynamic select list. Do you think this is possible? Perhaps I misread the >> file you have sent me a link to. >> Thanks, >> Katherine >> >> On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning >> wrote: >> >>> Hi Katherine, >>> >>> have a look at this one using repeats: >>> >>> https://github.com/bgruening/galaxytools/blob/master/tools/d >>> eseq2/deseq_helper.py >>> >>> Ciao, >>> Bjoern >>> >>> >>> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu: >>> > Hello Galaxy Community, >>> > I was wondering if anyone had ever come across a situation where they >>> > have had to pass the contents of a repeat parameter to a code file in a >>> > Galaxy tool config? Is there any way to do this? >>> > Katherine >>> > >>> > >>> > ___ >>> > 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: >>> > https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >>> > >>> >> >> > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Hi Bjorn, > Thank you for taking the time to reply to my question. I don't think this > quite fits what I am trying to accomplish. I am trying to pass a set of > metadata key value pairs, where the user can have as many key value pairs > as they want, generated with a repeat parameter. I would need to pass the > entire contents of the repeat parameter to the code file to generate a > dynamic select list. Do you think this is possible? Perhaps I misread the > file you have sent me a link to. > Thanks, > Katherine > > On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning > wrote: > >> Hi Katherine, >> >> have a look at this one using repeats: >> >> https://github.com/bgruening/galaxytools/blob/master/tools/d >> eseq2/deseq_helper.py >> >> Ciao, >> Bjoern >> >> >> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu: >> > Hello Galaxy Community, >> > I was wondering if anyone had ever come across a situation where they >> > have had to pass the contents of a repeat parameter to a code file in a >> > Galaxy tool config? Is there any way to do this? >> > Katherine >> > >> > >> > ___ >> > 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: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > >> > > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
Hi Katherine, have a look at this one using repeats: https://github.com/bgruening/galaxytools/blob/master/tools/deseq2/deseq_helper.py Ciao, Bjoern Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu: > Hello Galaxy Community, > I was wondering if anyone had ever come across a situation where they > have had to pass the contents of a repeat parameter to a code file in a > Galaxy tool config? Is there any way to do this? > Katherine > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
Ah - I understand what you mean now. Using the code tag is discouraged, but you may find some of these examples useful for what you are trying to do: https://github.com/galaxyproject/galaxy/issues/2714 I hope that helps, Peter On Thu, Sep 1, 2016 at 2:37 PM, Katherine Beaulieu wrote: > > > On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu > wrote: >> >> Hi Peter, >> The code file tag is generally used in populating select lists. So >> basically you have a function from a code file that is loaded before runtime >> of the tool and you can dynamically load content based on that function and >> you can pass it parameters from your tool but I'm wondering how you would >> pass it the contents of a repeat parameter. >> This is how the code file tag works: >> https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code >> Thanks, >> Katherine >> >> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock >> wrote: >>> >>> I'm not quite sure what you mean by a "code file", but if you >>> mean using the tag, here's an example: >>> >>> >>> https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml >>> >>> I am using a Cheetah syntax for loop to access each entry >>> in a repeat parameter. >>> >>> Peter >>> >>> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu >>> wrote: >>> > Hello Galaxy Community, >>> > I was wondering if anyone had ever come across a situation where they >>> > have >>> > had to pass the contents of a repeat parameter to a code file in a >>> > Galaxy >>> > tool config? Is there any way to do this? >>> > Katherine >>> > >>> > ___ >>> > 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: >>> > https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >> >> > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Hi Peter, > The code file tag is generally used in populating select lists. So > basically you have a function from a code file that is loaded before > runtime of the tool and you can dynamically load content based on that > function and you can pass it parameters from your tool but I'm wondering > how you would pass it the contents of a repeat parameter. > This is how the code file tag works: > https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code > Thanks, > Katherine > > On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock > wrote: > >> I'm not quite sure what you mean by a "code file", but if you >> mean using the tag, here's an example: >> >> https://github.com/peterjc/galaxy_mira/blob/master/tools/mir >> a4_0/mira4_de_novo.xml >> >> I am using a Cheetah syntax for loop to access each entry >> in a repeat parameter. >> >> Peter >> >> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu >> wrote: >> > Hello Galaxy Community, >> > I was wondering if anyone had ever come across a situation where they >> have >> > had to pass the contents of a repeat parameter to a code file in a >> Galaxy >> > tool config? Is there any way to do this? >> > Katherine >> > >> > ___ >> > 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: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
I'm not quite sure what you mean by a "code file", but if you mean using the tag, here's an example: https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml I am using a Cheetah syntax for loop to access each entry in a repeat parameter. Peter On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu wrote: > Hello Galaxy Community, > I was wondering if anyone had ever come across a situation where they have > had to pass the contents of a repeat parameter to a code file in a Galaxy > tool config? Is there any way to do this? > Katherine > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Send repeat parameter to code file for multiple select list
Hello Galaxy Community, I was wondering if anyone had ever come across a situation where they have had to pass the contents of a repeat parameter to a code file in a Galaxy tool config? Is there any way to do this? Katherine ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
