Re: [galaxy-user] barcode splitter files web based
Not all the files should be converted to datasets. It would be good if there is a restful API call for this saying "promote this output file to a dataset in the background". Then one could create HTML pages with many output files without cluttering the history and the user can herself decide which one to use for further analysis. This would be a more general solution. best, ido On Jul 10, 2013, at 6:11 PM, Jeremy Goecks wrote: >> Is there now a better way to import files that are actually already in >> galaxy? > > Not right now. The issue is that these files are part of a composite > datatype, and there's not currently a way to extract files from a composite > datatype and create Galaxy datasets for each. > > One potential solution is to transition this tool wrapper to produce a > variable number of output files using this approach: > > http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run > > Another is to extend the language constructs in a tool definition to make it > possible to use logical expressions (e.g. 3 * $inputs.length) to create a > certain number of output datasets. > >> Is there a trello card for this? > > Not that I can find, but one could be useful. > > J. > >> >> It would save our users a lot of time and nerves to be able to do this. >> >> thank you very much, >> ido >> >> >> >> On Mar 21, 2013, at 6:01 AM, Jennifer Jackson wrote: >> >>> Hi Ann, >>> >>> For just using the UI interface, I know of only one method (there may be >>> others): >>> >>> 1 - click on the "eye" icon to view the HTML barcode splitter output table >>> 2 - then for each individual file >>> a - right click to capture the "Copy Link Location" URL of the file >>> b - go to the tool "Get Data -> Upload File" and paste that URL into the " >>> URL/Text:" box >>> c - make other settings, like file format or database assignment >>> d - submit and the data will load as a dataset >>> >>> If there is a better way, we'll post an update. >>> Meanwhile, I hope this is helpful! >>> >>> Jen >>> Galaxy team >>> >>> >>> On 3/20/13 4:15 PM, Ann Holtz-Morris, M.S. wrote: HI, I’m trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don’t do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ >>> >>> -- >>> Jennifer Hillman-Jackson >>> Galaxy Support and Training >>> >>> http://galaxyproject.org >>> ___ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> ___ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to thi
Re: [galaxy-user] barcode splitter files web based
> Is there now a better way to import files that are actually already in galaxy? Not right now. The issue is that these files are part of a composite datatype, and there's not currently a way to extract files from a composite datatype and create Galaxy datasets for each. One potential solution is to transition this tool wrapper to produce a variable number of output files using this approach: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run Another is to extend the language constructs in a tool definition to make it possible to use logical expressions (e.g. 3 * $inputs.length) to create a certain number of output datasets. > Is there a trello card for this? Not that I can find, but one could be useful. J. > > It would save our users a lot of time and nerves to be able to do this. > > thank you very much, > ido > > > > On Mar 21, 2013, at 6:01 AM, Jennifer Jackson wrote: > >> Hi Ann, >> >> For just using the UI interface, I know of only one method (there may be >> others): >> >> 1 - click on the "eye" icon to view the HTML barcode splitter output table >> 2 - then for each individual file >> a - right click to capture the "Copy Link Location" URL of the file >> b - go to the tool "Get Data -> Upload File" and paste that URL into the " >> URL/Text:" box >> c - make other settings, like file format or database assignment >> d - submit and the data will load as a dataset >> >> If there is a better way, we'll post an update. >> Meanwhile, I hope this is helpful! >> >> Jen >> Galaxy team >> >> >> On 3/20/13 4:15 PM, Ann Holtz-Morris, M.S. wrote: >>> HI, >>> I’m trying to use the output files from barcode splitter. I know that the >>> command line as some wrappers made that take the output files and puts them >>> in the history. Is there anything similar for output files but for us >>> biologists who don’t do command line? J >>> >>> Thanks, >>> Ann >>> >>> CONFIDENTIALITY NOTICE: This electronic message is intended to be for the >>> use only of the named recipient, and may contain information that is >>> confidential or privileged. If you are not the intended recipient, you are >>> hereby notified that any disclosure, copying, distribution or use of the >>> contents of this message is strictly prohibited. If you have received this >>> message in error or are not the named recipient, please notify us >>> immediately by contacting the sender at the electronic mail address noted >>> above, and delete and destroy all copies of this message. Thank you. >>> >>> >>> ___ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> >>> http://lists.bx.psu.edu/ >> >> -- >> Jennifer Hillman-Jackson >> Galaxy Support and Training >> >> http://galaxyproject.org >> ___ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
Re: [galaxy-user] barcode splitter files web based
Is there now a better way to import files that are actually already in galaxy? Is there a trello card for this? It would save our users a lot of time and nerves to be able to do this. thank you very much, ido On Mar 21, 2013, at 6:01 AM, Jennifer Jackson wrote: > Hi Ann, > > For just using the UI interface, I know of only one method (there may be > others): > > 1 - click on the "eye" icon to view the HTML barcode splitter output table > 2 - then for each individual file > a - right click to capture the "Copy Link Location" URL of the file > b - go to the tool "Get Data -> Upload File" and paste that URL into the " > URL/Text:" box > c - make other settings, like file format or database assignment > d - submit and the data will load as a dataset > > If there is a better way, we'll post an update. > Meanwhile, I hope this is helpful! > > Jen > Galaxy team > > > On 3/20/13 4:15 PM, Ann Holtz-Morris, M.S. wrote: >> HI, >> I’m trying to use the output files from barcode splitter. I know that the >> command line as some wrappers made that take the output files and puts them >> in the history. Is there anything similar for output files but for us >> biologists who don’t do command line? J >> >> Thanks, >> Ann >> >> CONFIDENTIALITY NOTICE: This electronic message is intended to be for the >> use only of the named recipient, and may contain information that is >> confidential or privileged. If you are not the intended recipient, you are >> hereby notified that any disclosure, copying, distribution or use of the >> contents of this message is strictly prohibited. If you have received this >> message in error or are not the named recipient, please notify us >> immediately by contacting the sender at the electronic mail address noted >> above, and delete and destroy all copies of this message. Thank you. >> >> >> ___ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> >> http://lists.bx.psu.edu/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > > http://galaxyproject.org > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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-user] barcode splitter files web based
Hi Ann, For just using the UI interface, I know of only one method (there may be others): 1 - click on the "eye" icon to view the HTML barcode splitter output table 2 - then for each individual file a - right click to capture the "Copy Link Location" URL of the file b - go to the tool "Get Data -> Upload File" and paste that URL into the " URL/Text:" box c - make other settings, like file format or database assignment d - submit and the data will load as a dataset If there is a better way, we'll post an update. Meanwhile, I hope this is helpful! Jen Galaxy team On 3/20/13 4:15 PM, Ann Holtz-Morris, M.S. wrote: HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] barcode splitter files web based
HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
