Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
Hi Eric, the following should work, but is a real hack and not recommended, I think. https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/tools/parameters/dynamic_options.html code file=filter_genome_from_file.py param name = a label = one input format = data type = select dynamic_options = get_genomes_from_b($input_b) / Hope that will work for you. Bjoern Am 09.05.2014 16:42, schrieb Eric Rasche: Howdy All, I have a set of tools in two parts; the first part builds some databases and prepares some data structures, the second tool plots a subset of the data in the data structure. Specifically, the data in the structures are named genomes. The second tools needs to know which genomes, and I'd like to allow the user to be able to select from a list rather than typing in manually. Essentially what I'd like to be able to do is create a set of options for an input type=select from the results of executing a perl/python script. Is there any way to do this as of now? (ugly hacks are OK as this is a private server) -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
Hi Björn, Brilliant, thank you. That should be exactly what I need. Good to know all of these dynamic options filters exist. 09.05.2014, 15:54, Björn Grüning bjoern.gruen...@gmail.com: Hi Eric, the following should work, but is a real hack and not recommended, I think. https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/tools/parameters/dynamic_options.html code file=filter_genome_from_file.py param name = a label = one input format = data type = select dynamic_options = get_genomes_from_b($input_b) / Hope that will work for you. Bjoern Am 09.05.2014 16:42, schrieb Eric Rasche: Howdy All, I have a set of tools in two parts; the first part builds some databases and prepares some data structures, the second tool plots a subset of the data in the data structure. Specifically, the data in the structures are named genomes. The second tools needs to know which genomes, and I'd like to allow the user to be able to select from a list rather than typing in manually. Essentially what I'd like to be able to do is create a set of options for an input type=select from the results of executing a perl/python script. Is there any way to do this as of now? (ugly hacks are OK as this is a private server) -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Texas AM Univesity College Station, TX 77843 Ph: 4046922048 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
Hello, Eric, If the dynamic filters approach doesn't work out I can send you an approach that worked for me. It involves creating a tool-generated html report that contains a form which provides selection choices; and the form is set to submit to a 2nd tool of your choice tool (it contains the necessary fields to prime the tool). Not sure if it works on every breed of galaxy out there though. d. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
Hi Damion, Would you mind sharing your approach with us all? Thanks! Igor On May 9, 2014 1:51 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Hello, Eric, If the dynamic filters approach doesn't work out I can send you an approach that worked for me. It involves creating a tool-generated html report that contains a form which provides selection choices; and the form is set to submit to a 2nd tool of your choice tool (it contains the necessary fields to prime the tool). Not sure if it works on every breed of galaxy out there though. d. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
(in_file) as f_in:
for line in f_in:
rowdata = line.split('\t')
self.lookup['select_row'] +=1
tdTags = ''
for (col, field) in
enumerate(self.display_columns):
lookup['value'] = rowdata[col]
if (col == 0):
tdTags += 'tdinput
type=checkbox name=select value=%(select_row)s /%(value)s/td' %
self.lookup
else:
tdTags += 'td%(value)s/td'
% self.lookup
fp_out.write(\n\t\t\ttr%s/tr % tdTags)
...
fp_out.write(HTML_REPORT_FOOTER_FILE)
Tool B:
To keep it simple this one just does a single output dataset but I can show a
multiple output datset one, one for each set of query hits selected above if
you want. ' force_history_refresh=True ' is supposed to refresh the history
list after this executes all of its file writing but for some reason that
doesn't seem to work on my galaxy.
tool id=bccdcSelectSubset name=Select subsets
force_history_refresh=True
command interpreter=python
select_subset.py $input $output1 $output1.id $__new_file_path__
$incl_excl $select
/command
inputs
param name=input type=data format=tabular
label=Numbered tabular input file/
param name=incl_excl type=select format=text
label=Include or exclude selection?
option value=1Include selection/option
option value=0Exclude selection/option
/param
param name=select type=select multiple=true
display=checkboxes label=Select lines below
options from_dataset=input
column name=name index=0/
column name=value index=-1/
/options
/param
/inputs
outputs
data name=output1 format=tabular metadata_source=input
label=$tool.name on data $input.hid/
/outputs
help
.. class:: infomark
**What it does**
This tool produces a tabular file with a subset of the lines in its input
tabular file.
/help
/tool
And the python:
'''
python select_subset.py $input $output $incl_excl $select
'''
def stop_err( msg ):
sys.stderr.write(%s\n % msg)
sys.exit(1)
import sys
try:
input, output, incl_excl, select = sys.argv[1:]
except:
stop_err('you must provide the arguments input, output, incl_excl and
select.')
lines = {}
try:
lines = dict([(int(num), '') for num in select.split(',')])
except:
stop_err('Did you remember to number the input dataset?')
include = bool(int(incl_excl))
if include:
print 'Including selected lines...'
else:
print 'Excluding selected lines...'
f_out = open(output, 'w')
with open(input) as f_in:
for line in f_in:
cols = line.split('\t')
try:
num = int(cols[-1])
except:
stop_err('Did you remember to number the input dataset?')
if include:
if num in lines:
f_out.write('\t'.join(cols[:-1])+'\n')
else:
if not num in lines:
f_out.write('\t'.join(cols[:-1])+'\n')
f_in.close()
f_out.close()
print 'Done.'
From: Igor Topcin [igortop...@gmail.com]
Sent: Friday, May 09, 2014 1:05 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Inform tool interface with data specific to selected
dataset
Hi Damion,
Would you mind sharing your approach with us all?
Thanks!
Igor
On May 9, 2014 1:51 PM, Dooley, Damion
damion.doo...@bccdc.camailto:damion.doo...@bccdc.ca wrote:
Hello, Eric,
If the dynamic filters approach doesn't work out I can send you an approach
that worked for me. It involves creating a tool-generated html report that
contains a form which provides selection choices; and the form is set to submit
to a 2nd tool of your choice tool (it contains the necessary fields to prime
the tool). Not sure if it works on every breed of galaxy out there though.
d.
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
