Subtleties of <version_command> and escaping dollar signs
Hello all, I've just noticed that dollar signs for accessing environment variables must be escaped in the XML <command> tag, but must not be escaped in the <version_command> tag: https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91... I presume this is because <command> is parsed as a Cheetah template where dollar means a Python variable (like the input and output parameters), while for the <version_command> this does not happen? Has anyone else been caught out by this? Is it worth adding a note about this to the wiki? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Regards, Peter
Updated the wiki with this information. https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cversion_comm.... We got to get away from using the wiki page and start documenting this stuff in the XSD (https://github.com/JeanFred/Galaxy-XSD) directly and build the documentation from that. Maybe Eric or Björn will find a couple free hours some day to get that wiki information ported over :). Thanks for the catch Peter, John On Tue, Sep 1, 2015 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I've just noticed that dollar signs for accessing environment variables must be escaped in the XML <command> tag, but must not be escaped in the <version_command> tag:
https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91...
I presume this is because <command> is parsed as a Cheetah template where dollar means a Python variable (like the input and output parameters), while for the <version_command> this does not happen?
Has anyone else been caught out by this? Is it worth adding a note about this to the wiki? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Regards,
Peter ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Thanks John, I like that plan - is the XSD at the point where we can declare it in Galaxy Tool definition XML files s & validate them (via planemo or otherwise)? Peter On Wed, Sep 9, 2015 at 7:03 PM, John Chilton <jmchilton@gmail.com> wrote:
Updated the wiki with this information. https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cversion_comm....
We got to get away from using the wiki page and start documenting this stuff in the XSD (https://github.com/JeanFred/Galaxy-XSD) directly and build the documentation from that. Maybe Eric or Björn will find a couple free hours some day to get that wiki information ported over :).
Thanks for the catch Peter, John
On Tue, Sep 1, 2015 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I've just noticed that dollar signs for accessing environment variables must be escaped in the XML <command> tag, but must not be escaped in the <version_command> tag:
https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91...
I presume this is because <command> is parsed as a Cheetah template where dollar means a Python variable (like the input and output parameters), while for the <version_command> this does not happen?
Has anyone else been caught out by this? Is it worth adding a note about this to the wiki? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Regards,
Peter ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I would say it is a ways off yet, it doesn't even validate all proper XML yet, let alone have proper documentation tags. I was hoping adding the validation feature to planemo would spur some development on it, but it hasn't happened yet. Some people are trying it out though (https://github.com/galaxyproject/planemo/issues/298). Maybe the next mini hackathon/contribution event we organize should be on fixing that up. It is a really pretty easy way to contribute Galaxy IMO. -John On Wed, Sep 9, 2015 at 9:13 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks John,
I like that plan - is the XSD at the point where we can declare it in Galaxy Tool definition XML files s & validate them (via planemo or otherwise)?
Peter
On Wed, Sep 9, 2015 at 7:03 PM, John Chilton <jmchilton@gmail.com> wrote:
Updated the wiki with this information. https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cversion_comm....
We got to get away from using the wiki page and start documenting this stuff in the XSD (https://github.com/JeanFred/Galaxy-XSD) directly and build the documentation from that. Maybe Eric or Björn will find a couple free hours some day to get that wiki information ported over :).
Thanks for the catch Peter, John
On Tue, Sep 1, 2015 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I've just noticed that dollar signs for accessing environment variables must be escaped in the XML <command> tag, but must not be escaped in the <version_command> tag:
https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91...
I presume this is because <command> is parsed as a Cheetah template where dollar means a Python variable (like the input and output parameters), while for the <version_command> this does not happen?
Has anyone else been caught out by this? Is it worth adding a note about this to the wiki? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Regards,
Peter ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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John Chilton -
Peter Cock