Those macros look great and are exactly what I want :-) Thanx,
--Russell -----Original Message----- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: Tuesday, 1 April 2014 11:07 a.m. To: Smithies, Russell; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers? Hi Russell, Am 31.03.2014 23:46, schrieb Smithies, Russell: > Hi Bjoern, > Yes I'm aware of the macros but I've never managed to get them to work > ;-( Lets try to get them to work. It will do exactly what you want. The Homer Tools should be a easy enough to get you started: https://github.com/bgruening/galaxytools/tree/master/homer/tools > What I'd like is something like a php include tag to pull the contents of a > whole file into another file so I'm not repeating myself eg. for the database > lists in the megablast, blastn, and tblastn wrappers. > > Those select fields are nice, and in "ordinary" html and JQuery you > can do grouping but as far as I can tell it's not possible with > Galaxy/Cheetah XML templating - though we are a few versions behind so may > have overlooked recent updates. Not yet, but I think it would be easy to implement it. It's used in other areas of Galaxy a lot. Ciao, Bjoern > Thanx for your suggestions, > > --Russell > > -----Original Message----- > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn > Grüning > Sent: Tuesday, 1 April 2014 10:19 a.m. > To: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers? > > Hi Russell, > > would something like a http://ivaynberg.github.io/select2/ field work for you? > What do you mean with <include> tags? Are you aware of Galaxy macros? > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML > _Macros > > Cheers, > Bjoern > > Am 31.03.2014 22:58, schrieb Smithies, Russell: >> Does anyone have a workable solution to managing and displaying large lists >> in tool wrappers? >> eg. a database list containing hundreds of enteries in the blast+ tool? (we >> have 1,056 different blast databases). >> As a work-around we've split our blast databases into species (eg cow, >> sheep, fungus, clover, fish, rice, etc) then faked a multi-select to pull >> in those sub-database files with conditional selectors like this: >> >> <conditional name="db_opts"> >> <param name="db_opts_selector" type="select" label="Nucleotide >> Database Type"> >> <option value="pub" selected="True">Pub Databases</option> >> <option value="cattle">Cattle Databases</option> >> <option value="sheep">Sheep Databases</option> >> <option value="deer">Deer Databases</option> >> <option value="ruminant">Ruminant Databases</option> >> <option value="dog">Dog Databases</option> >> <option value="fungi">Fungi Databases</option> >> <option value="invertebrates">Invertebrates Databases</option> >> <option value="microarrays">Microarrays Databases</option> >> <option value="marsupials">Marsupials Databases</option> >> <option value="rodent">Rodent Databases</option> >> <option value="viruses">Viruses Databases</option> >> <option value="human">Human Databases</option> >> <option value="microarrays">Microarrays Databases</option> >> </param> >> >> <when value="ruminant"> >> <param name="database" type="select" label="Ruminant >> Nucleotide BLAST database" help=""> >> <options from_file="blastdb.ruminant.loc"> >> <column name="value" index="0"/> >> <column name="name" index="1"/> >> <column name="path" index="2"/> >> </options> >> </param> >> <param name="subject" type="hidden" value="" /> >> </when> >> >> >> <when value="misc"> >> <param name="database" type="select" label="Misc >> Nucleotide BLAST database" help=""> >> <options from_file="blastdb.misc.loc"> >> <column name="value" index="0"/> >> <column name="name" index="1"/> >> <column name="path" index="2"/> >> </options> >> </param> >> <param name="subject" type="hidden" value="" /> >> </when> >> >> >> We end up with a lot of duplication between tool wrappers (I've never >> managed to get an <include> tag working) and these aren't exactly simple to >> maintain so does anyone have a better solution? >> I had thought about tacking an extra field onto the .loc files with a >> "species" and doing some grouping with that but haven't progressed that idea >> very far yet. >> >> Any suggestions greatly appreciated :) >> >> Thanx, >> >> --Russell >> >> >> >> ___________________________________________________________ >> 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/ >> >> 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: > http://lists.bx.psu.edu/ > > 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
