tool which using web service
hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi
Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process.
can u help me how can i add such type of tool in Galaxy ?
Regards shashi ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser. i want to crate tool like this. can i get any documents for such type of tool. thanks for reply On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Sashi,
Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools
You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml.
Greg Von kuster
On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process.
can u help me how can i add such type of tool in Galaxy ?
Regards shashi ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hello Shashi, On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote:
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser.
Yes
i want to crate tool like this. can i get any documents for such type of tool.
Take a look at the <request_param_translation> tag explanation in our tool config syntax wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequest_par...
thanks for reply
On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Sashi,
Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools
You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml.
Greg Von kuster
On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process.
can u help me how can i add such type of tool in Galaxy ?
Regards shashi ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Shashi, You may find this wiki useful as well - sorry I missed it in my initial response. http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote:
Hello Shashi, On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote:
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser.
Yes
i want to crate tool like this. can i get any documents for such type of tool.
Take a look at the <request_param_translation> tag explanation in our tool config syntax wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequest_par...
thanks for reply
On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Sashi,
Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools
You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml.
Greg Von kuster
On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process.
can u help me how can i add such type of tool in Galaxy ?
Regards shashi ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi All, <tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> <description>table browser</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> <param name="sendToGalaxy" type="hidden" value="1" /> <param name="hgta_compressType" type="hidden" value="none" /> <param name="hgta_outputType" type="hidden" value="bed" /> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" > <value_translation> <value galaxy_value="auto" remote_value="primaryTable" /> <value galaxy_value="auto" remote_value="selectedFields" /> <value galaxy_value="wig" remote_value="wigData" /> <value galaxy_value="interval" remote_value="tab" /> <value galaxy_value="html" remote_value="hyperlinks" /> <value galaxy_value="fasta" remote_value="sequence" /> <value galaxy_value="gtf" remote_value="gff" /> </value_translation> </request_param> </request_param_translation> <uihints minwidth="800"/> <outputs> <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> </outputs> i want to add such type of tool . should i modify my application for to interact with galaxy.by this xml galaxy interact with other application. help me for adding such type of tool. thanks for reply On Thu, Aug 25, 2011 at 1:54 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Shashi,
You may find this wiki useful as well - sorry I missed it in my initial response.
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote:
Hello Shashi, On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote:
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser.
Yes
i want to crate tool like this. can i get any documents for such type of tool.
Take a look at the <request_param_translation> tag explanation in our tool config syntax wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequest_par...
thanks for reply
On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Sashi,
Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools
You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml.
Greg Von kuster
On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process.
can u help me how can i add such type of tool in Galaxy ?
Regards shashi ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (2)
-
Greg Von Kuster -
shashi shekhar