Creating new datatype with variable number of input files

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Creating new datatype with variable number of input files

Marcelk
Creating new datatype with variable number of input files

Hello,

This is the first question I ask on this list, please let me know if I'm 'doing it wrong'.

Currently I'm trying to implement a workflow that uses a sort of microarray data which consists of one CSV file for each experiment done. The first step in the workflow is to preprocess the data and merge all files into a single CSV file (using an R script). Now my question is, is it possible to supply the user a Galaxy 'upload file' interface where he/she can:
- enter the number of experiments done (thus number of files to upload)
- depending on the above, present one 'select file' button and a new metavalue used for naming the experiment
- directly execute an R script after pressing the 'Execute' button.
- add the single resulting file from this R script to the users history pane (an intermediate composite datatype holding all uploaded files and manually executing the script is fine as well)

If this is possible, could you please add a hint in the right direction, that would be very helpful! Also, just giving an example of a Galaxy workflow that does any of the mentioned would be great too!
However if this seems to be impossible to do, what are the alternatives? Maybe create my own webtool that does the above and link that to my Galaxy?

Thanks in advance for any replies.

- Marcel


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Re: Creating new datatype with variable number of input files

Edward Kirton
use the <repeat> tag to accept a list of infiles (and perhaps labels/timepoint/etc for each).

On Thu, Jan 13, 2011 at 6:22 AM, Kempenaar, M (med) <[hidden email]> wrote:

Hello,

This is the first question I ask on this list, please let me know if I'm 'doing it wrong'.

Currently I'm trying to implement a workflow that uses a sort of microarray data which consists of one CSV file for each experiment done. The first step in the workflow is to preprocess the data and merge all files into a single CSV file (using an R script). Now my question is, is it possible to supply the user a Galaxy 'upload file' interface where he/she can:
- enter the number of experiments done (thus number of files to upload)
- depending on the above, present one 'select file' button and a new metavalue used for naming the experiment
- directly execute an R script after pressing the 'Execute' button.
- add the single resulting file from this R script to the users history pane (an intermediate composite datatype holding all uploaded files and manually executing the script is fine as well)

If this is possible, could you please add a hint in the right direction, that would be very helpful! Also, just giving an example of a Galaxy workflow that does any of the mentioned would be great too!
However if this seems to be impossible to do, what are the alternatives? Maybe create my own webtool that does the above and link that to my Galaxy?

Thanks in advance for any replies.

- Marcel


De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.


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