Re: [galaxy-dev] checkboxes bug fix
Hi Kanwei, and thanks for your reply. I might have missed something really big but I'm kinda confused. I just double checked galaxy-dist and galaxy-central on bitbucket and I would like to know if I understood the code properly. Please correct me if I'm wrong. Let's look at the is_checked() method of the CheckboxField class in the lib/galaxy/web/form_builder.py file: If I'm not mistaken, it relies on the fact that if the checkbox is checked, the request will get two values (the checkbox and the hidden field) and if it is not, it will only get one value (the hidden field) since they bear the same name. The first part is the conditional that checks if the value is True: That means that there is only one value, so the checkbox must be unchecked. Therefore it tests the hidden field's value. It will return True if the hidden field's value is true. The second part is only executed if the above condition is false: this means either the checkbox is actually checked, or it is unchecked and the hidden field is false. It returns true if there are two values, i.e. if the checkbox is checked. If the hidden field is false, it will obviously return False. So, let's see both cases: - 1st case: the hidden field is true: If the checkbox is unchecked, the method will return True in the first part. If it is checked, it will also return True in the second part. - 2d case: the hidden field is false: If the checkbox is checked, like in the 1st case, the second part will return True. But if it is unchecked, the first part won't return anything since the received value is not True. So it will return the result of the second part which is false since False is not an instance of list. Now my questions are: Did I miss anything? If not, how can the first case work for you? Wouldn't there be some cases where a checkbox actually gives a value even if it is unchecked, and a field is ignored of there is already one with the same name? Thanks, L-A Le 24/08/2011 19:36, Kanwei Li a écrit : Hi L-A, I tried this on today's tip but could not reproduce the bug. I added your param param name=SQA type=boolean label=Run SolexaQA checked=true / to a tool and the correct value was produced on the command line and in the configfiles block as well. Re-running also gave the correct result. Are you still seeing this problem? Thanks, K 2011/8/15 Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise-amelie.schm...@embl.de Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected
Re: [galaxy-dev] Issue with file permissions of uploaded files
Thanks Nate, putting the upload_store_access directive into the nginx.conf indeed did the trick. Joern On 08/24/2011 07:45 PM, Nate Coraor wrote: You can also use the 'upload_store_access' option to the nginx upload module to make the files readable: http://www.grid.net.ru/nginx/upload.en.html --nate Kanwei Li wrote: Hi Joern, Would it be easier to just chmod the directories to reflect the new user? -K On Wed, Aug 24, 2011 at 4:42 AM, Joern Toedlingj.toedl...@imb-mainz.dewrote: Hi all, we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well. Now the Get data - Upload file does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_**store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole Upload file process fails. How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated. Thanks, Joern -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511 __ ___ 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/
[galaxy-dev] Offering a user-paid NGS analysis pipeline in the cloud
Dear Community, our lab has developed a NGS analysis pipeline for viral sequence analysis (both genomic resequencing and RNA-Seq, including some novel pathogen detection and viral quasi-species reconstruction approaches) that fulfills various analytical needs of our clinical cooperation partners. Since we believe that the pipeline might be of interest to the broader virological community we decided to integrate our workflow into Galaxy as a set of plugins. However, we do need our in-house computational capacities for our own analyses and are targeting people who do not have time and experience to set up their own Galaxy installation (for example, clinical virologists). Therefore, we would like to provide the finished product as a non-profit service in the cloud (for example, by using Amazon AWS, for which the Galaxy installation is pretty straightforward). We envision (or at least, hope) that the pipeline will be used heavily and would therefore like to transfer the costs for the used resources to the user (e.g., the clinical virologist) in a pay-as-you-go manner. Amazon offers its 'DevPay' service for these purpose, basically an infrastructure to bill users of an AWS application instead of the application provider. Again, we do not want to make any profit with this service, we just want people to pay for the cpu cycles they burn with as few hassles for us as possible. I could well imagine that other academic institutions have similar goals, e.g. being willing to offer their work for free without wanting to cover the costs for analysis resources. Does anyone have experience with similar kinds of setups and would like to offer advice? I am looking for hints about technical (e.g. how to best integrate a Cloud Galaxy with DevPay or similar) as well as legal hurdles that we might have to be careful about (e.g., are we in conflict with Open-Source Software Licenses if billing is involved, even if we do not make a profit etc.). Thanks a bunch! Grüße/Regards Sven-Eric Schelhorn -- Sven-Eric Schelhorn - http://mpi-inf.mpg.de/~sven Max Planck Institute for Informatics, Saarbrücken D3 - Computational Biology Applied Algorithmics smime.p7s Description: S/MIME cryptographic signature ___ 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/
Re: [galaxy-dev] Setting the output label based on input parameters?
Hi Kanwei, I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I couldn't get it to work. Also, in the example below the % should really be # right? Anything anyone can think of that I might be doing wrong? - Nik. On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li kan...@gmail.com wrote: Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: outputs %if param == True: data format=txt name=blah label=Label1 / %else data format=txt name=blah label=Label2 / %endif /outputs Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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/ ___ 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/
[galaxy-dev] creating new input/output formats
Hi all, Is there a relatively easy way to create your own input/output formats? Some of the formats from programs that I am trying to install on our local Galaxy do not exist as an option. Any ideas? - Nik. ___ 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/
Re: [galaxy-dev] creating new input/output formats
On 08/25/2011 12:12 PM, Nikhil Joshi wrote: Hi all, Is there a relatively easy way to create your own input/output formats? Some of the formats from programs that I am trying to install on our local Galaxy do not exist as an option. Any ideas? Hi have you looked at the following wiki page: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes Regards, Hans - Nik. ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy public instances: data and job quotas
Edward Kirton wrote: also, delete and purge a quota seems to have no effect. Hi Ed, They work for me. Note that delete/purge do not actually delete the db row itself. Delete marks the quota as deleted, and it no longer counts against any associated users. Purge removes all of the user/group associations, but it still remains in the database. If this isn't what you're seeing, can you send more details? Thanks for testing out new features! --nate On Wed, Aug 24, 2011 at 3:58 PM, Edward Kirton eskir...@lbl.gov wrote: i created some quotas which were assigned to groups (set as for yes, registered users) but apparently the groups didn't initially stick; i had to edit the quota after creation to reassign the group. On Fri, Aug 19, 2011 at 4:44 PM, Jennifer Jackson j...@bx.psu.edu wrote: Galaxy public instances: data and job quotas User data and job quota limits are now implemented at the public Galaxy Test instance http://test.g2.bx.psu.edu: http://galaxyproject.org/Test#**Quotashttp://galaxyproject.org/Test#Quotas While no quotas are currently implemented at the public Galaxy Main instance http://usegalaxy.org, we do ask that users stay within certain usage limits: http://galaxyproject.org/Main#**Quotashttp://galaxyproject.org/Main#Quotas If you find that you require additional resources, please consider the alternative Galaxy options explained at: http://galaxyproject.org/Big%**20Picture/Choiceshttp://galaxyproject.org/Big%20Picture/Choices Thanks for using Galaxy! __**_ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Setting the output label based on input parameters?
you can use label=${input.name}
Shaun
Quoting Nikhil Joshi najo...@ucdavis.edu on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I couldn't get it to work. Also, in the example below the % should
really be # right? Anything anyone can think of that I might be doing
wrong?
- Nik.
On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li kan...@gmail.com wrote:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to be
true.
- Nik.
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[galaxy-dev] filtering BED files by score in trackster
Hi The option to filter a BED file by the score in the visualization tool is brilliant! There is just one draw back: you can only filter by integers. Hence a score of 1.1 is the same as of score of 1.3. How difficult would it be to change the code in order to allow floats for the filter? Such a feature would help us a lot! I tried to dig into the visualization code...but I got lost. Thank you very much for your help Regards, Hans ___ 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/
Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Hi Curtis, Changeset details: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 We are planning on releasing a distribution within a week, so alternatively you could wait and pull from there, if you normally work from the galaxy-dist repository. And for everyone tracking this fix: the changeset was applied to the public Galaxy main instance yesterday (http://usegalaxy.org). Hope this helps! Jen Galaxy team On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: Jen, Can you also please describe the details of the fix? We need to fix the same issue in our local instance, but don't know if this was a fix to cuffdiff, or to galaxy. Which one should we be updating? Regards, Curtis -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user- boun...@lists.bx.psu.edu] On Behalf Of David K Crossman Sent: Friday, August 19, 2011 11:10 AM To: Jennifer Jackson Cc: galaxy-user (galaxy-u...@lists.bx.psu.edu) Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Jen, Thank you very much for the reply. I'm glad to know it is a known bug and not something on my side of things. So, would my analysis be affected if I did change the bam file Database/Build to the older tree shrew version found in the drop down list? What significance does this Database/Build box have in downstream analysis if you have your own fasta reference genome file and gtf annotation file that is being referenced instead of a locally cached one? I'm just trying to obtain a better understanding of the Database/Build box for analyses where I provide the fasta and gtf file. Thanks, David -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, August 19, 2011 9:20 AM To: David K Crossman Cc: galaxy-user (galaxy-u...@lists.bx.psu.edu) Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Hello David, This is a known bug. The correction is planned to be moved out onto the public Galaxy instance at the next update (within a week). Sorry for the current inconvenience, Best, Jen Galaxy team On 8/19/11 7:00 AM, David K Crossman wrote: Hello! I have an RNA-Seq project which consists of 5 samples from the species tree shrew. When uploading these fastq files into Galaxy, I chose unspecified (?) for the database/build since the latest tree shrew version is not in the drop down list. When using TopHat, Cufflinks/Compare I have selected a reference genome from my history instead of using a built-in index, as well as a gtf annotation file for Cufflinks/Compare and everything has been working fine. Now, I am at the Cuffdiff step and I am running into an error when setting it up to perform replicate analysis. When I select my TopHat accepted hits bam file I see a red X and the error: Unspecified genome build, click the pencil icon in the history item to set the genome build. Here's a screenshot of what I'm seeing: Since the latest reference genome for tree shrew wasn't listed, that's why I chose unspecified (?). Should I go back and edit these accepted hits bam files to say the Database/Build from the drop down list is Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)? I know that this is simple to change, but will this affect my results in any way? Any help/info would be greatly appreciated. Thanks, David ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
Re: [galaxy-dev] filtering BED files by score in trackster
The option to filter a BED file by the score in the visualization tool is brilliant! There is just one draw back: you can only filter by integers. Hence a score of 1.1 is the same as of score of 1.3. How difficult would it be to change the code in order to allow floats for the filter? Such a feature would help us a lot! Hi Hans, Good catch. The actual filtering step is fixed in galaxy-central changeset 5943:4f992059bfeb However, right now the slider/text still works in whole numbers most of the time; I'm not sure if it's feasible to have it work in tenths by default because that creates a huge number of possible slider states. If you didn't know, you can type in numbers to the slider labels, but that too rounds right now--this should probably be changed. Can you share a BED file with floats in the score column and I can play with it a bit? Thanks, J.___ 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/
Re: [galaxy-dev] Updated Cufflinks Wrapper
I just remembered what I did for the tophat wrapper. All I did was change the default behavior of the use coverage search option. I believe no is the default behavior and you have it as yes. From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, August 11, 2011 7:22 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Updated Cufflinks Wrapper Hi Ilya, Thanks for the contribution; most of it has been committed in changeset 0ef81af1de09 A couple notes: *I couldn't transplant your changes because your commit did not include recent changes to the Cufflinks wrapper. It appears you didn't merge correctly with the main repository at some point; please try to merge correctly as it speeds up the inclusion process significantly on our end. *I didn't include your changes to the Tophat wrapper because merging was incorrect and I couldn't figure out what you were trying to do. Let us know if you have any questions. Best, J. On Jul 27, 2011, at 7:26 PM, Chorny, Ilya wrote: I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.commailto:icho...@illumina.com 858-202-4582 ___ 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/
[galaxy-dev] Dataset Cleanup Question
I am running a local instance of Galaxy and I've been trying to sort out some issue with dataset cleanup. For the most part, things are working OK running the shell scripts in the recommended order: delete_userless_histories.sh purge_histories.sh purge_libraries.sh purge_folders.sh delete_datasets.sh purge_datasets.sh I have the number of days set to 10. When I look at the reports webapp however, it reports that there are 62 datasets were deleted more than 15 days ago, but have not yet been purged, disk space: 12975717335. These have stuck around now for 45 days (and counting). I have even tried running the scripts with the -f option to force galaxy to re-evaluate the datasets to no avail. Any suggestions? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University attachment: lparsons.vcf___ 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/
Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Hi Curtis, This is a good question. I'll post back to the list to (hopefully) gather some feedback. Thanks! Jen On 8/25/11 8:44 AM, Robert Curtis Hendrickson wrote: Wonderful. We're on galaxy-dist, but we can pull that patch. Are most local installs on Dist or Central? Thanks! Curtis -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, August 25, 2011 10:41 AM To: Robert Curtis Hendrickson Cc: David K Crossman; 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Hi Curtis, Changeset details: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 We are planning on releasing a distribution within a week, so alternatively you could wait and pull from there, if you normally work from the galaxy-dist repository. And for everyone tracking this fix: the changeset was applied to the public Galaxy main instance yesterday (http://usegalaxy.org). Hope this helps! Jen Galaxy team On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: Jen, Can you also please describe the details of the fix? We need to fix the same issue in our local instance, but don't know if this was a fix to cuffdiff, or to galaxy. Which one should we be updating? Regards, Curtis -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
[galaxy-dev] install with EPD python?
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed. ___ 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/
[galaxy-dev] Using tools on local instance of galaxy
Hi, We have a local instance of galaxy at our institution. I've been trying to use several existing wrappers for tools on galaxy right now, for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks through galaxy. I keep seeing the following error: An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found An error occurred running this job:Could not determine cufflinks version cufflinks -I 30 -F 0.05 -j 0.05 -p 4 -Q 0 -r Error running cufflinks. /bin/sh: cufflinks: not found This is despite the server having cufflinks and bwa available. Is there somewhere I need to put these executables? Any config/ini files that I need to update with the location of the executables? Thanks for any help, Dhivya ___ 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/
Re: [galaxy-dev] Setting the output label based on input parameters?
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to
be
true.
- Nik.
__**_
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[galaxy-dev] Storing a dict as metadata
I'd like to have a datatype with a dict as metadata. This dict() would store file offsets to enable seeking around to process different sections of the file. How do I add a dictionary data metadata element? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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/
