Bodged using string functions :-)

 

set $data = ''.join([line for line in ($seq_source_type.seq_paste.split()) if line[0] != ">"])

 

Removes the fasta header line and any white-space so I can pipe sequence directly to blastn.

Means users can quickly paste in a bit of sequence for blasting without first having to upload the data to their history.

 

--Russell

--

 

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Ross
Sent: Wednesday, 13 February 2013 1:34 p.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Fwd: Custom Cheetah filters?

 

Hi Russell,

 

There may be a better way, but this works for me in the Toolfactory to create space and special character free names?

 

<param name="foo" type="text" value="" label="Foo">

<sanitizer invalid_char="">

 <valid initial="string.letters,string.digits"/>

</sanitizer>

</param>

 

On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell <Russell.Smithies@agresearch.co.nz> wrote:

I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command.

Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example?

Perhaps there’s a better way of doing it – regex maybe?

 

Any ideas?

 

Thanx,

 

--Russell

--

 


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