different number output files generated based on user parameter
Thank you Shaun. That worked really good! One final question. What is the best way to generate output files dynamically by galaxy. That is if the user sets a parameter, say create bam file. Then the output file gets generated. If the same parameter is false or no, then galaxy does not generate this file. We tried using the when tags and the conditional tags inside the output tags with no luck. Thanks again and looking forward to your response. Victor On Feb 24, 2012, at 4:16 AM, SHAUN WEBB wrote:
Hi Victor,
this is how I have implemented this:
<param name="sample" type="text" format="txt" label="Sample label" />
<data format="tabular" name="filename" label="${sample}.genes-results" />
Shaun
Quoting VICTOR M RUOTTI wisc-mail <ruotti@wisc.edu> on Thu, 23 Feb 2012 13:06:23 -0600:
Hi Peter,Thanks for the quick feedback. Sorry if I wasn't clear. Yes, I asking on how to set the labels for a file so instead of <data format="tabular" name="filename" label="genes-results"/> we can have a variable that comes from the interface set by the user so it can be like this? Say the user set the name from a text box to be "S" We can have S saved as $prefix, something like below. <data format="tabular" name="$prefix.filename" label="$prefix.genes-results"/>
The files then will be labeled: S.genes-results They still be called dataset_547.dat but labeled based on the user's input?
Victor
On 02/23/12, Peter Cock wrote:
On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruotti <ruotti@wisc.edu> wrote:
Hi, I hope someone can help me on how to implement this into a wrapper.
This kind of question is normally redirected to the galaxy-dev list.
We would like to add an option so the user can set a sample name which then be used for the prefix of the output files names.
You have no control over the file names at all - Galaxy will assign something like database/files/000/dataset_547.dat automatically. The user never sees the file names anyway.
Are you asking about how to control the description/caption shown to the user in Galaxy?
Peter
___________________________________________________________ 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:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hi Victor Have you looked at the wiki page: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files "Variable Static Outputs determined by parameter values" is probably what you want Regards, Hans On 02/24/2012 10:16 PM, Victor Ruotti wrote:
Thank you Shaun. That worked really good!
One final question. What is the best way to generate output files dynamically by galaxy. That is if the user sets a parameter, say create bam file. Then the output file gets generated. If the same parameter is false or no, then galaxy does not generate this file.
We tried using the when tags and the conditional tags inside the output tags with no luck. Thanks again and looking forward to your response.
Victor
On Feb 24, 2012, at 4:16 AM, SHAUN WEBB wrote:
Hi Victor,
this is how I have implemented this:
<param name="sample" type="text" format="txt" label="Sample label" />
<data format="tabular" name="filename" label="${sample}.genes-results" />
Shaun
Quoting VICTOR M RUOTTI wisc-mail<ruotti@wisc.edu> on Thu, 23 Feb 2012 13:06:23 -0600:
Hi Peter,Thanks for the quick feedback. Sorry if I wasn't clear. Yes, I asking on how to set the labels for a file so instead of <data format="tabular" name="filename" label="genes-results"/> we can have a variable that comes from the interface set by the user so it can be like this? Say the user set the name from a text box to be "S" We can have S saved as $prefix, something like below. <data format="tabular" name="$prefix.filename" label="$prefix.genes-results"/>
The files then will be labeled: S.genes-results They still be called dataset_547.dat but labeled based on the user's input?
Victor
On 02/23/12, Peter Cock wrote:
On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruotti<ruotti@wisc.edu> wrote:
Hi, I hope someone can help me on how to implement this into a wrapper.
This kind of question is normally redirected to the galaxy-dev list.
We would like to add an option so the user can set a sample name which then be used for the prefix of the output files names.
You have no control over the file names at all - Galaxy will assign something like database/files/000/dataset_547.dat automatically. The user never sees the file names anyway.
Are you asking about how to control the description/caption shown to the user in Galaxy?
Peter
___________________________________________________________ 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:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
participants (2)
-
Hans-Rudolf Hotz -
Victor Ruotti