Re: [galaxy-dev] Tool XML parameter options from locally stored files
Hi.
I'm still searching for a solution to this problem.
Currently we have to implement a tool to read the GTF file selected
via a from_data_table parameter and output a list of feature types.
Secondly we have a second tool that reads this file using a
from_dataset parameter so the user can select a specific datatype.
Not really ideal, I would prefer to do this in one tool if possible.
If I could reference the file chosen in the first select then this
should work.
For instance in the output data tags I can put label=${gtf.value}
and it returns the name of the selected file from the datatable.
If I do the same in inputs section: options from_file=${gtf.value}
galaxy tries to find the file [galaxy_dir]/tool-data/${gtf.value}.
So the solution would ideally look like this:
param name=gtf type=select label=GTF File --gtf
options from_data_table=pycrac_gtf/ !--link to .loc file with
gtf file per species --
/param
param name=feature type=select label=Select feature
options from_file=${gtf.value}
column name=name index=2/
column name=value index=2/
filter type=unique_value name=unique column=1/
/options
/param
Hope that makes sense.
Thanks
Shaun
Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Fri, 15 Jul 2011
10:17:44 +0100:
Hi Greg,
thanks for the suggestion. This line doesn't seem to work:
options from_file=some_value
Galaxy looks for a file at galaxy_dir/tool-data/some_value rather
than the value given in the .loc file
I would also like to be able to use the galaxy data tables rather
then referring directly to a .loc file.
Any ideas?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 10:28:30 -0400:
Hi Shaun,
This should be possible. It's been quite a long time since I
worked on tools, so maybe others can provide better assistance if I
am incorrect here. You'll need to have a conditional something
like the following ( not tested whatsoever ):
conditional name=selected_file_select_list
param name=selected_gtf_file type=select label=Gtf
file by species
options from_file=some_file
column name=name index=2/
column name=some_value index=1/
/options
/param
when value=some_value
param name=values_from_selected_gtf_file
type=select label=Values from selected gtf file /
options from_file=some_value
column name=name index=2/
column name=some_value index=1/
/options
/when
/conditional
On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote:
Hi Greg, I'm not sure if this answers my question. Using
options_from_file is fine if I want to refer to the same file each
time.
In this case I want the first select to choose which gtf file to
look at (by species) and the second select to pull options (gtf
annotation types) from this file.
So I would somehow have to reference the file using the first
parameter rather than giving a hard-coded path.
Is that possible?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011
09:23:19 -0400:
Hello Shaun,
Use the 'from_file' option. The referenced file should be in the
~/tool-data directory in the Galaxy root. There are several
example tools in the distribution that use this option. Here is
the example code from the annotation profiler tool:
param name=table_names type=drill_down display=checkbox
hierarchy=recurse multiple=true label=Choose Tables to Use
help=Selecting no tables will result in using all tables.
from_file=annotation_profiler_options.xml/
and here is an example from the microbial import tool:
param name=kingdom type=select label=Select the Desired
Kingdom
options from_file=microbial_data.loc startswith=ORG
column name=name index=3/
column name=value index=3/
filter type=unique_value name=unique column=3/
/options
/param
On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote:
Hi,
I am trying to write a tool xml file and want to do the following:
I have a number of GTF files stored locally and referenced in a
data table. I give the user a drop down list of those available
using the following code:
param name=gtf type=select label=GTF File
options from_data_table=gtf_files/
/param
I then want them to choose an annotation type based on those
present in the selected gtf file above. It seems simple enough
to do this if the gtf file is in your history already:
param name=feature type=select multiple=true
label=Extract features
options from_dataset=gtf
column name=name index=2/
column name=value index=2/
filter type=unique_value name=unique column=2/
/options
/param
But is there a way to query locally stored files via
datatables/.loc files to pull out options when the file is
dynamically chosen
Re: [galaxy-dev] Tool XML parameter options from locally stored files
Hi Greg, thanks for the suggestion. This line doesn't seem to work: options from_file=some_value Galaxy looks for a file at galaxy_dir/tool-data/some_value rather than the value given in the .loc file I would also like to be able to use the galaxy data tables rather then referring directly to a .loc file. Any ideas? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 10:28:30 -0400: Hi Shaun, This should be possible. It's been quite a long time since I worked on tools, so maybe others can provide better assistance if I am incorrect here. You'll need to have a conditional something like the following ( not tested whatsoever ): conditional name=selected_file_select_list param name=selected_gtf_file type=select label=Gtf file by species options from_file=some_file column name=name index=2/ column name=some_value index=1/ /options /param when value=some_value param name=values_from_selected_gtf_file type=select label=Values from selected gtf file / options from_file=some_value column name=name index=2/ column name=some_value index=1/ /options /when /conditional On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote: Hi Greg, I'm not sure if this answers my question. Using options_from_file is fine if I want to refer to the same file each time. In this case I want the first select to choose which gtf file to look at (by species) and the second select to pull options (gtf annotation types) from this file. So I would somehow have to reference the file using the first parameter rather than giving a hard-coded path. Is that possible? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 09:23:19 -0400: Hello Shaun, Use the 'from_file' option. The referenced file should be in the ~/tool-data directory in the Galaxy root. There are several example tools in the distribution that use this option. Here is the example code from the annotation profiler tool: param name=table_names type=drill_down display=checkbox hierarchy=recurse multiple=true label=Choose Tables to Use help=Selecting no tables will result in using all tables. from_file=annotation_profiler_options.xml/ and here is an example from the microbial import tool: param name=kingdom type=select label=Select the Desired Kingdom options from_file=microbial_data.loc startswith=ORG column name=name index=3/ column name=value index=3/ filter type=unique_value name=unique column=3/ /options /param On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote: Hi, I am trying to write a tool xml file and want to do the following: I have a number of GTF files stored locally and referenced in a data table. I give the user a drop down list of those available using the following code: param name=gtf type=select label=GTF File options from_data_table=gtf_files/ /param I then want them to choose an annotation type based on those present in the selected gtf file above. It seems simple enough to do this if the gtf file is in your history already: param name=feature type=select multiple=true label=Extract features options from_dataset=gtf column name=name index=2/ column name=value index=2/ filter type=unique_value name=unique column=2/ /options /param But is there a way to query locally stored files via datatables/.loc files to pull out options when the file is dynamically chosen by a different parameter? This code is also wrapped in a conditional, I'm not sure if that will affect anything. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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
Re: [galaxy-dev] Tool XML parameter options from locally stored files
Hello Shaun, Use the 'from_file' option. The referenced file should be in the ~/tool-data directory in the Galaxy root. There are several example tools in the distribution that use this option. Here is the example code from the annotation profiler tool: param name=table_names type=drill_down display=checkbox hierarchy=recurse multiple=true label=Choose Tables to Use help=Selecting no tables will result in using all tables. from_file=annotation_profiler_options.xml/ and here is an example from the microbial import tool: param name=kingdom type=select label=Select the Desired Kingdom options from_file=microbial_data.loc startswith=ORG column name=name index=3/ column name=value index=3/ filter type=unique_value name=unique column=3/ /options /param On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote: Hi, I am trying to write a tool xml file and want to do the following: I have a number of GTF files stored locally and referenced in a data table. I give the user a drop down list of those available using the following code: param name=gtf type=select label=GTF File options from_data_table=gtf_files/ /param I then want them to choose an annotation type based on those present in the selected gtf file above. It seems simple enough to do this if the gtf file is in your history already: param name=feature type=select multiple=true label=Extract features options from_dataset=gtf column name=name index=2/ column name=value index=2/ filter type=unique_value name=unique column=2/ /options /param But is there a way to query locally stored files via datatables/.loc files to pull out options when the file is dynamically chosen by a different parameter? This code is also wrapped in a conditional, I'm not sure if that will affect anything. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ Greg Von Kuster Galaxy Development Team g...@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] Tool XML parameter options from locally stored files
Hi Shaun, This should be possible. It's been quite a long time since I worked on tools, so maybe others can provide better assistance if I am incorrect here. You'll need to have a conditional something like the following ( not tested whatsoever ): conditional name=selected_file_select_list param name=selected_gtf_file type=select label=Gtf file by species options from_file=some_file column name=name index=2/ column name=some_value index=1/ /options /param when value=some_value param name=values_from_selected_gtf_file type=select label=Values from selected gtf file / options from_file=some_value column name=name index=2/ column name=some_value index=1/ /options /when /conditional On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote: Hi Greg, I'm not sure if this answers my question. Using options_from_file is fine if I want to refer to the same file each time. In this case I want the first select to choose which gtf file to look at (by species) and the second select to pull options (gtf annotation types) from this file. So I would somehow have to reference the file using the first parameter rather than giving a hard-coded path. Is that possible? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 09:23:19 -0400: Hello Shaun, Use the 'from_file' option. The referenced file should be in the ~/tool-data directory in the Galaxy root. There are several example tools in the distribution that use this option. Here is the example code from the annotation profiler tool: param name=table_names type=drill_down display=checkbox hierarchy=recurse multiple=true label=Choose Tables to Use help=Selecting no tables will result in using all tables. from_file=annotation_profiler_options.xml/ and here is an example from the microbial import tool: param name=kingdom type=select label=Select the Desired Kingdom options from_file=microbial_data.loc startswith=ORG column name=name index=3/ column name=value index=3/ filter type=unique_value name=unique column=3/ /options /param On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote: Hi, I am trying to write a tool xml file and want to do the following: I have a number of GTF files stored locally and referenced in a data table. I give the user a drop down list of those available using the following code: param name=gtf type=select label=GTF File options from_data_table=gtf_files/ /param I then want them to choose an annotation type based on those present in the selected gtf file above. It seems simple enough to do this if the gtf file is in your history already: param name=feature type=select multiple=true label=Extract features options from_dataset=gtf column name=name index=2/ column name=value index=2/ filter type=unique_value name=unique column=2/ /options /param But is there a way to query locally stored files via datatables/.loc files to pull out options when the file is dynamically chosen by a different parameter? This code is also wrapped in a conditional, I'm not sure if that will affect anything. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ Greg Von Kuster Galaxy Development Team g...@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/
