edit file in galaxy

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edit file in galaxy

Jasper Jan Koehorst
Hello,

I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file.

Is this possible?

Thanks,

jasper



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Re: edit file in galaxy

Björn Grüning-2
Hi Jasper,

that is not possible at the moment, because it would break workflows. Nevertheless, it is easy to write such a tool if you really would like to do that. Have you looked at the text manipulation tools? Many modification, if not all, can be done with this tools.

Cheers,
Bjoern

P.S. The galaxy-user ML is deprecated and questions like this should be ask at https://biostar.usegalaxy.org/


2014-05-13 8:31 GMT+02:00 Koehorst, Jasper <[hidden email]>:
Hello,

I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file.

Is this possible?

Thanks,

jasper



___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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To search Galaxy mailing lists use the unified search at:

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___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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Re: edit file in galaxy

Jen Hillman-Jackson
In reply to this post by Jasper Jan Koehorst
Hi Jasper,

Bjorn is correct, using the Text manipulation tools is usually the best
way to edit files. But along with that, there is also a way to add in
content. Using the tool "Get Data -> Upload File" you can just
type/paste in content in the box and it will upload as a file. Spaces
can be converted to tabs if you want.

Sometimes this is useful for adding a line to the start of a file. It
can be used to add a column of data, but only if your file is not very
large (not too many rows). The general idea is that you can load in the
extra data, then add it to other files using "Concatenate" or "Paste" or
even "Join" if there is a common fields. Then you can use "Cut" to
select columns/rearrange the data.

Good luck and do join us on Biostar!
https://wiki.galaxyproject.org/Support#Biostar

Jen
Galaxy team

On 5/12/14 11:31 PM, Koehorst, Jasper wrote:

> Hello,
>
> I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file.
>
> Is this possible?
>
> Thanks,
>
> jasper
>
>
>
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
>
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
>
> For discussion of local Galaxy instances and the Galaxy
> source code, please use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: edit file in galaxy

Ay Ayy
In reply to this post by Jasper Jan Koehorst
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[hidden email]
Find me at about.me/uy73


-----Original Message-----
From: Koehorst, Jasper <[hidden email]>
To: galaxy-user <[hidden email]>
Sent: Tue, May 13, 2014 3:18 pm
Subject: [galaxy-user] edit file in galaxy

Boxbe Koehorst, Jasper ([hidden email]) is not on your Guest List | Approve sender | Approve domain
Hello,

I am generating files but sometimes I want to add something to the text file 
generated. I would like to do this within galaxy instead of downloading, 
modifying, uploading the file.

Is this possible?

Thanks,

jasper



___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
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For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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To search Galaxy mailing lists use the unified search at:

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Re: edit file in galaxy

Jen Hillman-Jackson
Hello,

You can use the tools in the groups "Text Manipulation", "Filter and Sort", and the "Get Data -> Upload File -> paste text into the box".

There are also other replies along the same thread previously posted to this list, but incorporated into Galaxy Biostar. For example: https://biostar.usegalaxy.org/p/6666/#6676
Use the search function at the top or see the right side bar for others that are similar.

This mailing list is being phased out and Galaxy Biostar is replacing it. Please post new questions there. Here is how to get started: https://wiki.galaxyproject.org/Support#Biostar

If you do need to post a reply here, please be sure to not include the extra graphics or links, just the question in regular text.

Best,

Jen
Galaxy team

On 5/15/14 6:23 PM, Ay Ayy wrote:
Hello,

I am generating files but sometimes I want to add something to the text file 
generated. I would like to do this within galaxy instead of downloading, 
modifying, uploading the file.

Is this possible?

Thanks,

jasper



___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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