syntax and #if and #for statements within the <command> tag
Hi all, So I've gotten some simple custom tools to work on our local Galaxy, however, I am having trouble figuring out exactly how the syntax works for the commands and lines within the <command> tag. E.g., I've seen #if and #for statements and also lines using functions like "str", but I can't really find any documentation about exactly how the syntax works. It kinda seems like PHP syntax, but not quite? Anyways, any help would be highly appreciated. Thanks! - Nik. On Wed, Aug 3, 2011 at 6:20 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Nikhil,
I am responsible for the tool shed ( both implementation as well as documentation ), and finally got a chance to get the wiki started yesterday (that's why it is currently lacking in information). I will be working on the wiki as the top priority now, so it should be fairly useful within the next day or so. In the meantime, please feel free to direct any questions to the mail list, and I'll answer them in short order.
Getting started with the tool shed is fairly straight-forward. You can browse existing repositories to see how others have designed their file hierarchies. Many very good examples of repositories have been created by Peter Cock ( his public username on the tool shed is peterjc ), so browse some of his repositories to get an idea. Here's a good example of a repo that includes a single tool that uses a .loc file:
Contents: effectivet3<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> tool-data/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> effectiveT3.loc.sample<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> tools/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> protein_analysis/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> effectiveT3.py<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> effectiveT3.txt<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#> effectiveT3.xml<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
You can browse repos without authenticating, but in order to create a repo, you'll need to authenticate, so create an account on the tool shed if you don't yet have one.
Regarding your questions about the "XML format for the XML file", the repository is simply a container for files of any type ( tool configs, data, binaries, python scripts, exported Galaxy workflows, etc ), so the repository itself has no requirement for XML formats, etc. Generally, XML files will simply be the Galaxy tool config, the syntax of which is defined on our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Thanks very much for you interest in the tool shed,
Greg Von Kuster
On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote:
Hi all,
I have been using Galaxy for a few years now and I am about to start creating my own repositories for the new Tool Shed. However, I can't seem to find any good documentation on how to do that exactly. Can someone point me in the right direction? I need to figure out the best way to organize a repository, the XML format for the XML file, and any other important things that I might need to know? Is there a good resource for all that? The wiki has a section entitled "Create a new repository", but there is nothing in it. Any help would highly appreciated. Thanks!
- Nik.
-- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.edu
Nik, The syntax is Cheetah, (http://www.cheetahtemplate.org/). Also, see more about some of the extra tags available on the galaxy wiki, http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_... -Dannon On Aug 9, 2011, at 6:29 PM, Nikhil Joshi wrote:
Hi all,
So I've gotten some simple custom tools to work on our local Galaxy, however, I am having trouble figuring out exactly how the syntax works for the commands and lines within the <command> tag. E.g., I've seen #if and #for statements and also lines using functions like "str", but I can't really find any documentation about exactly how the syntax works. It kinda seems like PHP syntax, but not quite? Anyways, any help would be highly appreciated. Thanks!
- Nik.
On Wed, Aug 3, 2011 at 6:20 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Nikhil,
I am responsible for the tool shed ( both implementation as well as documentation ), and finally got a chance to get the wiki started yesterday (that's why it is currently lacking in information). I will be working on the wiki as the top priority now, so it should be fairly useful within the next day or so. In the meantime, please feel free to direct any questions to the mail list, and I'll answer them in short order.
Getting started with the tool shed is fairly straight-forward. You can browse existing repositories to see how others have designed their file hierarchies. Many very good examples of repositories have been created by Peter Cock ( his public username on the tool shed is peterjc ), so browse some of his repositories to get an idea. Here's a good example of a repo that includes a single tool that uses a .loc file:
Contents: effectivet3 tool-data/ effectiveT3.loc.sample tools/ protein_analysis/ effectiveT3.py effectiveT3.txt effectiveT3.xml
You can browse repos without authenticating, but in order to create a repo, you'll need to authenticate, so create an account on the tool shed if you don't yet have one.
Regarding your questions about the "XML format for the XML file", the repository is simply a container for files of any type ( tool configs, data, binaries, python scripts, exported Galaxy workflows, etc ), so the repository itself has no requirement for XML formats, etc. Generally, XML files will simply be the Galaxy tool config, the syntax of which is defined on our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Thanks very much for you interest in the tool shed,
Greg Von Kuster
On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote:
Hi all,
I have been using Galaxy for a few years now and I am about to start creating my own repositories for the new Tool Shed. However, I can't seem to find any good documentation on how to do that exactly. Can someone point me in the right direction? I need to figure out the best way to organize a repository, the XML format for the XML file, and any other important things that I might need to know? Is there a good resource for all that? The wiki has a section entitled "Create a new repository", but there is nothing in it. Any help would highly appreciated. Thanks!
- Nik.
-- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.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:
participants (2)
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Dannon Baker -
Nikhil Joshi