how to get raw input from GUI

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how to get raw input from GUI

Rui Wang
Hi,

I am working on a wrapper for gatk and including 

            <repeat name="filters" title="filter names and expressions" help="--filterName, --filterExpression">
                <param name="filter_name" type="text" value="" title="Filter name to be included in the analysis" />
                <param name="filter_exp" type="data" value="" title="Filter expression to be included in the analysis" />
            </repeat>

in it, however, when I reference it using

${filter.filter_exp}

it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX

is there a way that I could keep the original text string 'FS > 30.0'? I did a quick lookup online but didn't see anything in cheetah's user guide or other places.

Thanks,
Rui



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Re: how to get raw input from GUI

Eric Rasche-2
Hi Rui,

I believe you're looking for a sanitizer.
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?#A.3Csanitizer.3E_tag_set

Hope this helps.

On 14. juni 2016 00:12, Beginner TI wrote:
Hi,

I am working on a wrapper for gatk and including 

            <repeat name="filters" title="filter names and expressions" help="--filterName, --filterExpression">
                <param name="filter_name" type="text" value="" title="Filter name to be included in the analysis" />
                <param name="filter_exp" type="data" value="" title="Filter expression to be included in the analysis" />
            </repeat>

in it, however, when I reference it using

${filter.filter_exp}

it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX

is there a way that I could keep the original text string 'FS > 30.0'? I did a quick lookup online but didn't see anything in cheetah's user guide or other places.

Thanks,
Rui




___________________________________________________________
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:
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]

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Re: how to get raw input from GUI

Rui Wang
Hi Eric,

Thanks for the info!

I'll look into it. :-)
Rui

On Mon, Jun 13, 2016 at 5:20 PM, Eric Rasche <[hidden email]> wrote:
Hi Rui,

I believe you're looking for a sanitizer.
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?#A.3Csanitizer.3E_tag_set

Hope this helps.


On 14. juni 2016 00:12, Beginner TI wrote:
Hi,

I am working on a wrapper for gatk and including 

            <repeat name="filters" title="filter names and expressions" help="--filterName, --filterExpression">
                <param name="filter_name" type="text" value="" title="Filter name to be included in the analysis" />
                <param name="filter_exp" type="data" value="" title="Filter expression to be included in the analysis" />
            </repeat>

in it, however, when I reference it using

${filter.filter_exp}

it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX

is there a way that I could keep the original text string 'FS > 30.0'? I did a quick lookup online but didn't see anything in cheetah's user guide or other places.

Thanks,
Rui




___________________________________________________________
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/

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]


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Re: how to get raw input from GUI

Dooley, Damion
In reply to this post by Rui Wang
A general note, besides <sanitize> which sounds like a fine choice, a
technique I've used where the form's input might have some wonky
characters in it, including carriage returns, but these need to be
received and processed via a command line, is to use encode():

$rules.encode('base64').replace('\n','')

Then over in receiving python script

Rules = rulesparam.decode('base64')

D.


>Message: 3
>Date: Mon, 13 Jun 2016 17:12:05 -0700
>From: Beginner TI <[hidden email]>
>To: "[hidden email]" <[hidden email]>
>Subject: [galaxy-dev] how to get raw input from GUI
>Message-ID:
> <[hidden email]>
>Content-Type: text/plain; charset="utf-8"
>
>Hi,
>
>I am working on a wrapper for gatk and including
>
>            <repeat name="filters" title="filter names and expressions"
>help="--filterName, --filterExpression">
>                <param name="filter_name" type="text" value=""
>title="Filter name to be included in the analysis" />
>                <param name="filter_exp" type="data" value=""
>title="Filter
>expression to be included in the analysis" />
>            </repeat>
>
>in it, however, when I reference it using
>
>${filter.filter_exp}
>
>it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX
>
>is there a way that I could keep the original text string 'FS > 30.0'? I
>did a quick lookup online but didn't see anything in cheetah's user guide
>or other places.
>
>Thanks,
>Rui

___________________________________________________________
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:
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