Re: [galaxy-dev] . Output file to history (Sebastian Luna Valero)

2014-03-31 Thread John Chilton
I have opened a pull request that I believe could significantly ease the operations like this (for instance grabbing a directory of similar output files all of the same type based on a pattern specified by the tool instead of by Galaxy). There are lots of details of in the pull request body and som

Re: [galaxy-dev] . Output file to history (Sebastian Luna Valero)

2014-03-22 Thread Ross
Hi, Jun and Sebastian, This is not trivial, but it is already being done with some tools using the method described at https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Single_history_output_Html_file_with_links_to_any_number_of_output_files_and_images if that can solve your pro

Re: [galaxy-dev] . Output file to history (Sebastian Luna Valero)

2014-03-22 Thread Jun Fan
Hi Sebastian, I am not an expert in galaxy developing. So the following content is just my personal opinion. I do not think it is possible to meet you requirement. I reckon Galaxy searches the certain folder, defined in the universal_wsgi.ini by a parameter called #collect_outputs_from =

[galaxy-dev] Output file to history

2014-03-21 Thread Jennifer Jackson
Hi Sebastian, I'm going to move this over to the galaxy-...@bx.psu.edu mailing list so that it reaches the development community effectively. I personally do not know the answer, but I am sure we can get you some help. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists On 3/2

Re: [galaxy-dev] Output file naming

2012-10-26 Thread James Taylor
On Fri, Oct 26, 2012 at 3:47 PM, Peter Cock wrote: > i.e. This isn't something each tool author should be doing, > but something general that should be in Galaxy itself. Yes, we would very much like a visual/graphical indicator of dataset ancestry, and possibly an alternative history view that wa

Re: [galaxy-dev] Output file naming

2012-10-26 Thread Peter Cock
On Fri, Oct 26, 2012 at 7:53 PM, Anthonius deBoer wrote: > and if you use something like ... > > I do this for all the tools in galaxy (bit of a pain, but worth it) so they > produce more intelligent names than "12: X on data 10" etc. > > Thon These kind of tricks are quite handy, but in general

Re: [galaxy-dev] Output file naming

2012-10-26 Thread Anthonius deBoer
and if you use something like;label="#echo os.path.splitext ( str ( $input.name ) ) [ 0 ] #-BWA.bam"You can change "SomeFile.fastq" into "SomeFile-BWA.bam".This allows you to remove the extension (.fastq in this case), insert some extra text after the original name and set the right extension (Not

Re: [galaxy-dev] Output file naming

2012-10-26 Thread Joachim Jacob
Hi, You can use label="$input.name" Cheers, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 10/26/2012 04:38 PM, Darin wrote: Hello, I'm new to Galaxy, and I've been asked

[galaxy-dev] Output file naming

2012-10-26 Thread Darin
Hello, I'm new to Galaxy, and I've been asked to tweak some tools so that output file names are related to input file names. For example, an input file of myData.abc might lead to an output file named myData_afterMyTool.xyz. I think the user is really just interested in the labels showing u

Re: [galaxy-dev] output file

2012-07-19 Thread Edward Kirton
change your tool to use explicitly named output folder and files bash mytool.sh $input $output1.extra_files_path $output1 $output2 where $output1.extra_files_path will be a folder (e.g. working dir) $output1, $output2, etc. are files that are to be brought into your history in galaxy, to be used

Re: [galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners

2012-07-11 Thread Nate Coraor
On Jul 5, 2012, at 9:21 PM, Rob Syme wrote: > Hi all. > > When I run the FastQC tool using the default local job runner, it produces a > folder of files with permission 664: > > -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png > -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 er

[galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners

2012-07-05 Thread Rob Syme
Hi all. When I run the FastQC tool using the default local job runner, it produces a folder of files with permission 664: -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 error.png -rw-rw-r-- 1 galaxy galaxy 7.5K Jul 5 17:29 fastqc_

[galaxy-dev] output file

2012-05-07 Thread 張詩婷
Hi, After execution, my tool created many files in a directory , how can I to find this directory? command: bash mytool.sh $input ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscription

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-14 Thread Tanguy Le Carrour
Hi, Thanks for the tips and CC! Cheers, Tanguy ___ 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.p

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-13 Thread Dannon Baker
On 04/13/2011 12:30 PM, Dave Walton wrote: Is there anyway to access the value of fields that are part of the workflow. Taking the "Input Dataset" example, that is an input file that goes into my next module. I'd like to grab the name of that input file, and then append it with a new extensio

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-13 Thread Dave Walton
I get it now!! I did my Rename Dataset/output_file with a variable ${input}. I chose that because I thought that would give me the name of the input file to that module, which I'm looking to carry on through out the run of my workflow (though actually I'd like the file name minus the file ext

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-13 Thread Dannon Baker
Ahh, I understand your confusion now. The previous bit you pointed out was an error indeed, but not the one you were running into. The variable name should be whatever you want it to be, it doesn't have to map to an existing value like "Input Dataset", but there's an issue with the way the ta

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-13 Thread Matthew Conte
Hi Dannon, Sorry, I guess I still don't quite get it. So I should keep the Input Dataset name the default which is "Input Dataset". In the next subsequent step in the workflow I then edit step actions Rename Dataset/output_file with "${Input Dataset} groomed", for example. This gives me the sam

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-13 Thread Dannon Baker
The input dataset steps do not use workflow parameters as they don't actually create output datasets, but rather act as more of a temporary handle. Remove the parameter tags from the input steps and just referring to those same parameter names in the subsequent steps you wanted to use them wit

Re: [galaxy-dev] Output file naming / dataset's label

2011-04-12 Thread Matthew Conte
I'd like to do the same thing that Tanguy described. I'm trying to figure out the syntax to this within the workflow editor, but can't quite get it right. In your example Dannon, would you just set ${dataset_name} as the "Name" for your "Input dataset" to capture the input dataset name as a varia