How to build an application that uses a set of files?
Hello, I would like to get advice how to implement the following application into Galaxy: We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9. Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file. How would the xml look? Thanks! George Weingart
Are these 17 files fairly dynamic - i.e. are they going to depend on previous steps in a history or user uploads - or are they literally just 17 more or less fixed files associated with that tool and every user should see roughly the same 17 options. -John On Thu, Aug 21, 2014 at 3:03 PM, George Weingart <george.weingart@gmail.com> wrote:
Hello,
I would like to get advice how to implement the following application into Galaxy:
We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9.
Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file.
How would the xml look?
Thanks! George Weingart
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They are totally dynamic. Say all the files of tabular type that the User has at the moment. On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <jmchilton@gmail.com> wrote:
Are these 17 files fairly dynamic - i.e. are they going to depend on previous steps in a history or user uploads - or are they literally just 17 more or less fixed files associated with that tool and every user should see roughly the same 17 options.
-John
On Thu, Aug 21, 2014 at 3:03 PM, George Weingart <george.weingart@gmail.com> wrote:
Hello,
I would like to get advice how to implement the following application into Galaxy:
We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9.
Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file.
How would the xml look?
Thanks! George Weingart
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hmm... in that case I think you can just create a multiple input data parameter. <input type="data" format="tabular" multiple="true" name="inputs" label="blah" /> You can iterate through the files in your <command> tag and pass them to your merge.py file: <command interpreter="python">merge.py #for $input in $inputs# $input #end for# ... </command> This works unless you literally need 9 files - this input type doesn't support min/max right now. (There is a Trello card that includes adding such functionality if you want to vote on it https://trello.com/c/lp5YmA1O). I hope this helps - let me know if this is not quite right. -John On Thu, Aug 21, 2014 at 3:30 PM, George Weingart <george.weingart@gmail.com> wrote:
They are totally dynamic. Say all the files of tabular type that the User has at the moment.
On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <jmchilton@gmail.com> wrote:
Are these 17 files fairly dynamic - i.e. are they going to depend on previous steps in a history or user uploads - or are they literally just 17 more or less fixed files associated with that tool and every user should see roughly the same 17 options.
-John
On Thu, Aug 21, 2014 at 3:03 PM, George Weingart <george.weingart@gmail.com> wrote:
Hello,
I would like to get advice how to implement the following application into Galaxy:
We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9.
Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file.
How would the xml look?
Thanks! George Weingart
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi John, Worked on first try! Thanks!!!!! George Weingart PhD On Thu, Aug 21, 2014 at 12:43 PM, John Chilton <jmchilton@gmail.com> wrote:
Hmm... in that case I think you can just create a multiple input data parameter.
<input type="data" format="tabular" multiple="true" name="inputs" label="blah" />
You can iterate through the files in your <command> tag and pass them to your merge.py file:
<command interpreter="python">merge.py #for $input in $inputs# $input #end for# ... </command>
This works unless you literally need 9 files - this input type doesn't support min/max right now. (There is a Trello card that includes adding such functionality if you want to vote on it https://trello.com/c/lp5YmA1O).
I hope this helps - let me know if this is not quite right.
-John
They are totally dynamic. Say all the files of tabular type that the User has at the moment.
On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <jmchilton@gmail.com> wrote:
Are these 17 files fairly dynamic - i.e. are they going to depend on previous steps in a history or user uploads - or are they literally just 17 more or less fixed files associated with that tool and every user should see roughly the same 17 options.
-John
On Thu, Aug 21, 2014 at 3:03 PM, George Weingart <george.weingart@gmail.com> wrote:
Hello,
I would like to get advice how to implement the following application into Galaxy:
We have a set of say, 17 tabular files, we would like to present
On Thu, Aug 21, 2014 at 3:30 PM, George Weingart <george.weingart@gmail.com> wrote: them
to the User and allow him to select a subset of them, say 9.
Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file.
How would the xml look?
Thanks! George Weingart
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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George Weingart -
John Chilton