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
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
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 =
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
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
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
and if you use something like;label="#echo os.path.splitext ( str ( $input.name ) ) [ 0 ] #-BWA.bam"You can change "SomeFile.fastq" into "SomeFile-BWA.bam".This allows you to remove the extension (.fastq in this case), insert some extra text after the original name and set the right extension (Not
Hi,
You can use label="$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
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
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
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
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_
Hi,
After execution, my tool created many files in a directory , how can I to
find this directory?
command: bash mytool.sh $input
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Hi,
Thanks for the tips and CC!
Cheers,
Tanguy
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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
I get it now!!
I did my Rename Dataset/output_file with a variable ${input}.
I chose that because I thought that would give me the name of the input file to
that module, which I'm looking to carry on through out the run of my workflow
(though actually I'd like the file name minus the file ext
Ahh, I understand your confusion now. The previous bit you pointed out
was an error indeed, but not the one you were running into. The
variable name should be whatever you want it to be, it doesn't have to
map to an existing value like "Input Dataset", but there's an issue with
the way the ta
Hi Dannon,
Sorry, I guess I still don't quite get it. So I should keep the Input
Dataset name the default which is "Input Dataset". In the next subsequent
step in the workflow I then edit step actions Rename Dataset/output_file
with "${Input Dataset} groomed", for example. This gives me the sam
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
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
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