Hi,
Is there a way to use validator or perhaps filter options to avoid the
selection of the same dataset twice in different parameters of a tool.
E.g. a tool has 2 data type parameters of the same type, but it should not be
possible for the user to set both parameters to the same dataset. So
The same here.
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
___
Please keep all replies on the list by
Hi,
I assume you mean to group the parameters visually. What I have seen
people doing is adding HTML code to the value of the label attribute of
a param tag set, like ending the label with e.g. br/hr.
Otherwise, if the two groups of parameters are mutually exclusive, you
can use the
I really could not find this. Anybody willing to show me? :-)
Cheers,
Joachim
BTW: pity that they disabled the issue tracker on BitBucket... Hope it
will be replaced by something similar soon. I feel like this community
needs an issue tracker, besides a help communication channel like this
Hi Alfredo,
I also asked the same question before without any response:
http://dev.list.galaxyproject.org/Reserved-variables-in-param-tags-td465640
2.html
But I met Dannon Baker on the Swiss galaxy workshop in Bern and explained
this problem to him. He said it should not be a big problem to fix
Hi Brad,
Thanks for reporting this error, it has been fixed in changeset
7902:2d12f10c87c7 and will be available in the next distribution.
Thanks for using Galaxy,
Dan
On Oct 13, 2012, at 10:30 PM, Langhorst, Brad wrote:
Error - type 'exceptions.NameError': global name 'string' is not
Hello Joachim,
I did the test here, but there appears no effect when I add tags to label
the value you entered.
Do you have any examples?
Maybe I might be doing wrong.
Hugs.
2012/10/15 Joachim Jacob joachim.ja...@vib.be
Hi,
I assume you mean to group the parameters visually. What I have
Hi,
You might have a look to the GMAP aligner wrapper in the toolshed
http://toolshed.g2.bx.psu.edu/. Apparently you have to use the html
codes for the symbols, instead of the symbols themselves
GMAP example:
label=lt;H2gt;Input Sequenceslt;/H2gt;Select an mRNA or EST dataset
to map /
Here is an implementation of the implicit multi-file composite
datatypes piece of that idea. I think the implicit parallelism may be
harder.
https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes/compare
Jorrit do you have any objection to me trying to get this included in
On Mon, Oct 15, 2012 at 5:12 AM, Joachim Jacob joachim.ja...@vib.be wrote:
I really could not find this. Anybody willing to show me? :-)
Sure, go here:
http://lists.bx.psu.edu/options/galaxy-dev
After entering your credentials, Set Digest Mode is the second
option from the top.
Hope it helps,
Thanks! Now I wonder of course how I missed it. But I was stuck
apparently at http://dev.list.galaxyproject.org/
Thanks again for your time,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
Very Good!
It worked, it helped me a lot.
Thank you.
2012/10/15 Joachim Jacob joachim.ja...@vib.be
Hi,
You might have a look to the GMAP aligner wrapper in the toolshed
http://toolshed.g2.bx.psu.edu/**. Apparently you have to use the html
codes for the symbols, instead of the symbols
Hi all;
Open Bio regularly organizes hackathon coding sessions in conjunction
with the Bioinformatics Open Source Conference. The goal is to get
together biologists writing open source code, provide a room and
internet, and encourage fun collaborative coding. We've had successful
two day
Hello,
I've installed a tool to my local Galaxy installation via my local
ToolShed. I would like to run this tool locally, and not have it submitted
to the grid.
I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners]
section.
The tool id directly from the tool.xml file and the id
Be aware that this may not work in future versions of Galaxy, and
probably won't work in some places already (e.g. trackster).
If this is a common need, one option would be to create a new type of
grouping construct that would simply be a labeled group. In the config
this would be:
group
Hi,
i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain
perl scripts, that wraps around other dependencies (e.g. Bowtie). The
idea was to include the perl-scripts directly in the galaxy-wrapper and
update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml
file.
I managed to fix my problem.
I modified the CCAT wrapper to output the CCAT log file to Galaxy,
then got this at the end:
reading tag files..
0 tags in L1, 0 tags in L2.
tag file error!
So there was an error when running the CCAT binary, but the CCAT
wrapper thinks it succeeded and tries to
In the Add or Replace Groups tool for picard, if the read group platform unit
is left blank, the read group sample name is lost as well. Must all the read
group tags be set with this tool? Can some of them remain blank?
David Hoover
Helix Systems Staff, CIT/NIH
Hi John,
I tried your galaxy-central-homogeneous-composite-datatypes implementation,
works great thank you (and Jorrit).
A couple of fixes:
1. Add multi_upload.xml to too_conf.xml
2. lib/galaxy/tools/parameters/grouping.py line 322 (in get_filenames( context
)) -
if ftp_files is not
Hi all,
I managed to break a toolshed-installed tool by fiddling with the
files under shed_tools. This led to a situation in which the Galaxy
admin interface claims the tool is still installed, but can't find any
files for it. I manually put the repository files where I think they
should go, but
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