Multiple fastq files per forward/reverse mates (tophat and related tools)
I want to customize the tophat and related interfaces to allow more than one fastq file per fwd/rev set as is allowed and very helpful in the CLI version: $ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq Is there a way to select multiple items from a dropdown menu or can/should i convert that part of the interface to a text input field so I can simply feed the command a list of files like on the command line? This last method seems like it might be a little unsafe though. But even if its not, it divorces the file management from the history which seems like its not a good idea. Has anyone done this? Thanks, Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*
Hi Gus, for parameters of the type "select" you can enable the option to select multiple options. However, this isn't really suitable for files, I think. I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files. Sarah On 07/11/2011 02:18 AM, W. Augustine Dunn III wrote:
I want to customize the tophat and related interfaces to allow more than one fastq file per fwd/rev set as is allowed and very helpful in the CLI version: $ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq
Is there a way to select multiple items from a dropdown menu or can/should i convert that part of the interface to a text input field so I can simply feed the command a list of files like on the command line? This last method seems like it might be a little unsafe though. But even if its not, it divorces the file management from the history which seems like its not a good idea.
Has anyone done this?
Thanks,
Gus
-- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. /-Stephen Jay Gould/
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I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files.
Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag. Gus, if you end up modifying the Tophat wrapper to support multiple input datasets, please submit a patch or fork galaxy-central via bitbucket and I'll integrate these enhancements into the Galaxy code base as this would be nice functionality to have. Best, J.
First off thank you heartily for pointing me in the right direction here. It SEEMS like i have managed to accomplish this. Meaning: i finally got the run to get past the parsing of the config file and now have a process running on the cpu and the server log shows a command line string that matches what I was trying to get. However I am VERY new at the whole Cheetah craziness, so I DEF want you folks to double check my work. I would LOVE to contribute a patch but have these questions and concerns: 1. I cloned the 'dist' branch not the 'central' branch originally and am not sure if my tophat_wrapper.xml version will clash with any that have been included in the central branch, I would assume that the system's diff capabilities SHOULD be able to sort this out but I am WAY more familiar with git than hg. 2. I have created a bitbucket account and supplied my pubkey, but I dont see anything on the wiki that describes how a person gets "push" or similar permissions on the galaxy project what is the procedure for correctly submitting these types of piecemeal single file changes? Thanks again for your help and I am very excited to have a chance to give back! Gus On Mon, Jul 11, 2011 at 8:51 AM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files.
Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag.
Gus, if you end up modifying the Tophat wrapper to support multiple input datasets, please submit a patch or fork galaxy-central via bitbucket and I'll integrate these enhancements into the Galaxy code base as this would be nice functionality to have.
Best, J.
-- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*
Gus, Good to hear about your progress. Please send me a patch of your changes and I'll take a look. You can create a patch using Mercurial from the command line as follows. % hg diff > tophat.patch Thanks, J. On Jul 13, 2011, at 7:37 PM, W. Augustine Dunn III wrote:
First off thank you heartily for pointing me in the right direction here.
It SEEMS like i have managed to accomplish this. Meaning: i finally got the run to get past the parsing of the config file and now have a process running on the cpu and the server log shows a command line string that matches what I was trying to get. However I am VERY new at the whole Cheetah craziness, so I DEF want you folks to double check my work.
I would LOVE to contribute a patch but have these questions and concerns: I cloned the 'dist' branch not the 'central' branch originally and am not sure if my tophat_wrapper.xml version will clash with any that have been included in the central branch, I would assume that the system's diff capabilities SHOULD be able to sort this out but I am WAY more familiar with git than hg. I have created a bitbucket account and supplied my pubkey, but I dont see anything on the wiki that describes how a person gets "push" or similar permissions on the galaxy project what is the procedure for correctly submitting these types of piecemeal single file changes? Thanks again for your help and I am very excited to have a chance to give back!
Gus
On Mon, Jul 11, 2011 at 8:51 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files.
Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag.
Gus, if you end up modifying the Tophat wrapper to support multiple input datasets, please submit a patch or fork galaxy-central via bitbucket and I'll integrate these enhancements into the Galaxy code base as this would be nice functionality to have.
Best, J.
-- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. -Stephen Jay Gould
participants (3)
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Jeremy Goecks -
Sarah Diehl -
W. Augustine Dunn III