[galaxy-dev] Adding options to a tool
Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Adding options to a tool
Hello Scott, the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. The tophat tool is hosted here: https://toolshed.g2.bx.psu.edu/view/devteam/tophat and developed here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat However the first thing I would check is whether the newer version of the tool (named tophat2) that we recently updated would suit your needs. You can try it on our Test instance here: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 Please let me know if you have any questions and thank you for using Galaxy. Martin, Galaxy Team On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi scott.b.szakony...@nd.edu wrote: Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Adding options to a tool
Hi Scott and just double checking, in case you do have an 'old' Galaxy installation: after modifying the xml file (I assume you are talking about tophat_wrapper.xml?): Have you re-loaded the tool? click on 'Reload a tool's configuration' on the administration menu and select the tool Hans-Rudolf Reload a tool's configuration On 02/11/2015 11:00 PM, Martin Čech wrote: Hello Scott, the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. The tophat tool is hosted here: https://toolshed.g2.bx.psu.edu/view/devteam/tophat and developed here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat However the first thing I would check is whether the newer version of the tool (named tophat2) that we recently updated would suit your needs. You can try it on our Test instance here: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 Please let me know if you have any questions and thank you for using Galaxy. Martin, Galaxy Team On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi scott.b.szakony...@nd.edu mailto:scott.b.szakony...@nd.edu wrote: Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu http://crc.nd.edu/ _ 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/ https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ 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/
