Auto detection of output format Galaxy custom tool
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
Hi Katherine, The file datatype have support on galaxy plataform!? If not, you add the datatype what you need in your galaxy instance!? Att. On Wed, Jun 29, 2016, 11:16 AM Katherine Beaulieu < katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine ___________________________________________________________ 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/
-- Best regards, *Léo Biscassi*
Have you invented your own file format, or are you using an existing file format defined within Galaxy? The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method. Peter On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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/
Hmm, I must have some sort of other logic error which is preventing the detection of the format. Thanks for the information! On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Have you invented your own file format, or are you using an existing file format defined within Galaxy?
The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method.
Peter
Hi everyone, I am looking to auto-detect the file format of a file outputted by a
tool I have written. Does anyone have any idea how to do this? I have
On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote: python tried
setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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/
The auto-detection is only used when importing a file into Galaxy (e.g. by uploading it). If you are writing a tool which produces output in your format, then the tool's XML should specify that output format. Which of these are you trying to do? Or both? Peter On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hmm, I must have some sort of other logic error which is preventing the detection of the format. Thanks for the information!
On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Have you invented your own file format, or are you using an existing file format defined within Galaxy?
The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method.
Peter
On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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 am trying to import a file into galaxy. On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
The auto-detection is only used when importing a file into Galaxy (e.g. by uploading it).
If you are writing a tool which produces output in your format, then the tool's XML should specify that output format.
Which of these are you trying to do? Or both?
Peter
On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hmm, I must have some sort of other logic error which is preventing the detection of the format. Thanks for the information!
On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Have you invented your own file format, or are you using an existing file format defined within Galaxy?
The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method.
Peter
On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if
you
would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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/
OK. What happens? Can you select the correct datatype in the upload tool? If not, check the file format definition as some file formats are configured not to appear here. Are you leaving the datatype as "auto"? If so, does Galaxy fail to identify the file, and leave it as the default generic "data" type, or does Galaxy mis-identify it as another type? Have you looked at the Galaxy logs while doing the upload? How is this file format defined in Galaxy? Did you add it? Can you test the Python code in the sniff function outside of Galaxy to confirm that works? If Galaxy wrongly picks another fileformat, check where in the datatypes_conf.xml is your file format listed? The order the sniffing functions are run is important. Peter On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
I am trying to import a file into galaxy.
On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
The auto-detection is only used when importing a file into Galaxy (e.g. by uploading it).
If you are writing a tool which produces output in your format, then the tool's XML should specify that output format.
Which of these are you trying to do? Or both?
Peter
On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hmm, I must have some sort of other logic error which is preventing the detection of the format. Thanks for the information!
On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Have you invented your own file format, or are you using an existing file format defined within Galaxy?
The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method.
Peter
On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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/
Ok, so I don't give the user the option to select the correct data type to reduce the amount of stuff the user has to know when using the tool. I do leave the format as auto and Galaxy just leaves it as the generic data type 'data'. As for how the format is defined in Galaxy, I'm not quite sure what the answer to this question is because I am just testing the tool with really simple text files, with extension .txt. and it can't seem to pick it up, it just leaves it as 'data'. Also not quite sure how to test the Python code in the sniff function outside of Galaxy... (only starting working with Galaxy 3 weeks ago). Let me know if I should provide you with the tool config file if that would be a little more useful. It's quite straightforward Thanks for helping with this. On Wed, Jun 29, 2016 at 11:16 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
OK. What happens?
Can you select the correct datatype in the upload tool? If not, check the file format definition as some file formats are configured not to appear here.
Are you leaving the datatype as "auto"? If so, does Galaxy fail to identify the file, and leave it as the default generic "data" type, or does Galaxy mis-identify it as another type?
Have you looked at the Galaxy logs while doing the upload?
How is this file format defined in Galaxy? Did you add it? Can you test the Python code in the sniff function outside of Galaxy to confirm that works?
If Galaxy wrongly picks another fileformat, check where in the datatypes_conf.xml is your file format listed? The order the sniffing functions are run is important.
Peter
I am trying to import a file into galaxy.
On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
The auto-detection is only used when importing a file into Galaxy (e.g. by uploading it).
If you are writing a tool which produces output in your format, then the tool's XML should specify that output format.
Which of these are you trying to do? Or both?
Peter
On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hmm, I must have some sort of other logic error which is preventing
detection of the format. Thanks for the information!
On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <
On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote: the p.j.a.cock@googlemail.com>
wrote:
Have you invented your own file format, or are you using an existing file format defined within Galaxy?
The Galaxy file formats with automatic detection are all defined via Python classes which define a sniff method.
Peter
On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to auto-detect the file format of a file outputted by
a
python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine
___________________________________________________________ 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/
Maybe sharing your tool XML file would be best - is it on GitHub? Peter On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Ok, so I don't give the user the option to select the correct data type to reduce the amount of stuff the user has to know when using the tool.
I do leave the format as auto and Galaxy just leaves it as the generic data type 'data'.
As for how the format is defined in Galaxy, I'm not quite sure what the answer to this question is because I am just testing the tool with really simple text files, with extension .txt. and it can't seem to pick it up, it just leaves it as 'data'. Also not quite sure how to test the Python code in the sniff function outside of Galaxy... (only starting working with Galaxy 3 weeks ago).
Let me know if I should provide you with the tool config file if that would be a little more useful. It's quite straightforward Thanks for helping with this.
Hi Katherine I presume this is related to the tool described here ( https://biostar.usegalaxy.org/p/18319/)? I think there is general interest in the creation of a tool like this - see the recent email from Miu ki Yip. If you could share the code and XML (e.g. via GitHub) perhaps we could assist with what you are trying to write. Peter On 30 June 2016 at 19:01, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Maybe sharing your tool XML file would be best - is it on GitHub?
Peter
On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Ok, so I don't give the user the option to select the correct data type to reduce the amount of stuff the user has to know when using the tool.
I do leave the format as auto and Galaxy just leaves it as the generic data type 'data'.
As for how the format is defined in Galaxy, I'm not quite sure what the answer to this question is because I am just testing the tool with really simple text files, with extension .txt. and it can't seem to pick it up, it just leaves it as 'data'. Also not quite sure how to test the Python code in the sniff function outside of Galaxy... (only starting working with Galaxy 3 weeks ago).
Let me know if I should provide you with the tool config file if that would be a little more useful. It's quite straightforward Thanks for helping with this.
___________________________________________________________ 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/
Hi Peter, I ending up finding a solution to my problem using this forum post: https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html. I just ended up using the really specific file output path and it started auto-detecting the file format. Thanks for your help it was much appreciated. On Thu, Jun 30, 2016 at 1:01 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Maybe sharing your tool XML file would be best - is it on GitHub?
Peter
On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Ok, so I don't give the user the option to select the correct data type to reduce the amount of stuff the user has to know when using the tool.
I do leave the format as auto and Galaxy just leaves it as the generic data type 'data'.
As for how the format is defined in Galaxy, I'm not quite sure what the answer to this question is because I am just testing the tool with really simple text files, with extension .txt. and it can't seem to pick it up, it just leaves it as 'data'. Also not quite sure how to test the Python code in the sniff function outside of Galaxy... (only starting working with Galaxy 3 weeks ago).
Let me know if I should provide you with the tool config file if that would be a little more useful. It's quite straightforward Thanks for helping with this.
I'm glad you could solve this - thanks for letting us know and linking to the old email discussion which helped. Peter On Thu, Jul 7, 2016 at 4:35 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi Peter, I ending up finding a solution to my problem using this forum post: https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html. I just ended up using the really specific file output path and it started auto-detecting the file format. Thanks for your help it was much appreciated.
participants (4)
-
Katherine Beaulieu -
Léo Biscassi -
Peter Cock -
Peter van Heusden