Re: [galaxy-dev] Managing large database lists in tool wrappers?
On 31.03.2014 22:58, 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). On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Russell, would something like a http://ivaynberg.github.io/select2/ field work for you? Which bit of that do you mean Bjoern? Galaxy already does searching within the drop down box (when the list is above some threshold in length) which is very handy. Mind you, we currently have under a hundred BLAST databases defined in our *.loc files, so this is an order of magnitude less than Russell's setup. 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 Since it looks like you are modifying the BLAST+ wrappers, they are already using Galaxy macros - you probably only need to change the ncbi_macros.xml file once and have this work on all of BLASTP, BLASTN, etc. i.e. Modify the input_conditional_nucleotide_db and input_conditional_protein_db definitions (and potentially the token @BLAST_DB_SUBJECT@ where those parameters are inserted in the the Cheetah command line template): https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml Regards, Peter ___ 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/
Re: [galaxy-dev] Managing large database lists in tool wrappers?
Hi, On 31.03.2014 22:58, 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). On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Russell, would something like a http://ivaynberg.github.io/select2/ field work for you? Which bit of that do you mean Bjoern? Galaxy already does searching within the drop down box (when the list is above some threshold in length) which is very handy. Yes, that was my intention. To point out that something like that should be possible. It new for me that there is a threshold to enable that mechanism. Mind you, we currently have under a hundred BLAST databases defined in our *.loc files, so this is an order of magnitude less than Russell's setup. We also have only 3x. So no problem until now. Ciao, Bjoern 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 Since it looks like you are modifying the BLAST+ wrappers, they are already using Galaxy macros - you probably only need to change the ncbi_macros.xml file once and have this work on all of BLASTP, BLASTN, etc. i.e. Modify the input_conditional_nucleotide_db and input_conditional_protein_db definitions (and potentially the token @BLAST_DB_SUBJECT@ where those parameters are inserted in the the Cheetah command line template): https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml Regards, Peter ___ 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/
[galaxy-dev] Managing large database lists in tool wrappers?
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=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays 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/
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=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays 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/
Re: [galaxy-dev] Managing large database lists in tool wrappers?
Hi Bjoern, Yes I'm aware of the macros but I've never managed to get them to work ;-( 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. 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=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays 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
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=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays 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
Re: [galaxy-dev] Managing large database lists in tool wrappers?
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=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays 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
