Tophat/Cuff Parameters

5.0 years ago by

United Kingdom

Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and "play" with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name "-r", etc. To see all of the parameters on the forms: 1. Tophat/2 - open "TopHat settings to use: Full parameter list" 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy- dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu> mailing list going forward. Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Irene Bassano • 90

Hello - Most of these are at defaults. The source code is the best place to find any that are hard-coded (if included, most likely done to manage resources). Again, any of of this could be modified if you have programming resource. The repository is owned by the devteam and in the Tool Shed, search with "cuff" here: http://usegalaxy.org/toolshed Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks again Jen, I just would like to get this point: if I want to modify them then I won't be using Galaxy right, since there are few of them I can modify. All I would like to know is: are the hidden/chosen/not accessible parameters CHOSEN by Galaxy? If yes, is there any chance to know what has been chosen for these parameters which are not visible? Or did I understand that are default as written in the manual? Hope it's clear, sorry for insisting but I need to know as I am doing an analysis for someone else and have to report all the options I have opted for! I cannot tell anything about those which are not listed I have read the link you sent me , but I cannot find all the missing options...I opened all the links on it an found only those already listed in the main cufflinks running page(see attachment).. Thanks again for your patience, Best, Irene To: Irene Bassano; 'galaxy-user@bx.psu.edu' Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hello - Most of these are at defaults. The source code is the best place to find any that are hard-coded (if included, most likely done to manage resources). Again, any of of this could be modified if you have programming resource. The repository is owned by the devteam and in the Tool Shed, search with "cuff" here: http://usegalaxy.org/toolshed Best, Jen Galaxy team Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and "play" with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name "-r", etc. To see all of the parameters on the forms: 1. Tophat/2 - open "TopHat settings to use: Full parameter list" 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy- dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu> mailing list going forward. Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Irene Bassano • 90

Hi, Yes, the .py part of the wrapper you attached is how the tool is implemented in Galaxy. The .xml is what is displayed on the tool form. Together, these execute the command string for the job. Knowing the parameters used for a job run is definitely important and this is included in the interface. If you click on the "info" icon, the small circle "i", for a dataset, the full command line is listed. Parameters set by the run are listed and can be compared to the manual. Anything not in the command string would be at default, just as if you were running the tool on the command line (not through Galaxy). This information captures execution parameters for reproducibility. Directly from the Galaxy run, but you can also use similar if you choose to run the tool on the command line (to use/add parameters not yet implemented in a Galaxy tool repository). There are a few tools that do not report the command line yet in the interface (older ones), but it can still be obtained independently by triggering an error, then submitting a bug report -> a cc copy is sent to the reporter that contains it. Just put in the comments to ignore the bug submission. Not an ideal method (will be addressed), but is open for anyone to use, any tool. Hopefully this helps! No parameters are hidden to my knowledge. Best, Jen Galaxy team

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks a lot Jen! Irene ________________________________________ To: Irene Bassano Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hi, Yes, the .py part of the wrapper you attached is how the tool is implemented in Galaxy. The .xml is what is displayed on the tool form. Together, these execute the command string for the job. Knowing the parameters used for a job run is definitely important and this is included in the interface. If you click on the "info" icon, the small circle "i", for a dataset, the full command line is listed. Parameters set by the run are listed and can be compared to the manual. Anything not in the command string would be at default, just as if you were running the tool on the command line (not through Galaxy). This information captures execution parameters for reproducibility. Directly from the Galaxy run, but you can also use similar if you choose to run the tool on the command line (to use/add parameters not yet implemented in a Galaxy tool repository). There are a few tools that do not report the command line yet in the interface (older ones), but it can still be obtained independently by triggering an error, then submitting a bug report -> a cc copy is sent to the reporter that contains it. Just put in the comments to ignore the bug submission. Not an ideal method (will be addressed), but is open for anyone to use, any tool. Hopefully this helps! No parameters are hidden to my knowledge. Best, Jen Galaxy team Thanks again Jen, I just would like to get this point: if I want to modify them then I wont be using Galaxy right, since there are few of them I can modify. All I would like to know is: are the hidden/chosen/not accessible parameters CHOSEN by Galaxy? If yes, is there any chance to know what has been chosen for these parameters which are not visible? Or did I understand that are default as written in the manual? Hope its clear, sorry for insisting but I need to know as I am doing an analysis for someone else and have to report all the options I have opted for! I cannot tell anything about those which are not listed I have read the link you sent me , but I cannot find all the missing optionsI opened all the links on it an found only those already listed in the main cufflinks running page(see attachment).. Thanks again for your patience, Best, Irene To: Irene Bassano; 'galaxy-user@bx.psu.edu<mailto:galaxy- user@bx.psu.edu="">' Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hello - Most of these are at defaults. The source code is the best place to find any that are hard-coded (if included, most likely done to manage resources). Again, any of of this could be modified if you have programming resource. The repository is owned by the devteam and in the Tool Shed, search with "cuff" here: http://usegalaxy.org/toolshed Best, Jen Galaxy team Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and play with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name "-r", etc. To see all of the parameters on the forms: 1. Tophat/2 - open "TopHat settings to use: Full parameter list" 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy- dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu> mailing list going forward. Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson 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<http: 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org <cufflinks.png>

ADD REPLY • link written 5.0 years ago by Irene Bassano • 90

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