How to prevent parsing ">" into "__lt_

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Question: How to prevent parsing ">" into "__lt__" in Galaxy wrapper

11 months ago by

md2587 • 10

md2587 • 10 wrote:

Hi,

I am writing Galaxy tool wrapper which should accept as an input regular expression for example like this: (?P<cell_1>.{16})(?P<umi_1>.{10})

But when I run the tool it is parsed into: (?P__lt__cell_1__gt__.__oc__16__cc__)(?P__lt__umi_1__gt__.__oc__10__cc__)

Any idea how should I prevent singes ">" to be parsed into __lt__ ?

Thanks, Marija

sanitize regular expression prevent wrapper • 279 views

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modified 11 months ago by Hotz, Hans-Rudolf • 1.8k • written 11 months ago by md2587 • 10

11 months ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Hi Marija

Special characters are sanitized for security purposes. See: ~/lib/galaxy/util/__init__.py for all the mapped characters.

Have a look at: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-sanitizer for ways to handle this on a per tool basis. However, keep in mind, that passing such characters unsanitized is a potential security risk.

Hope this helps Regards, Hans-Rudolf

PS: This is the same answer as here: https://biostar.usegalaxy.org/p/24057/

ADD COMMENT • link written 11 months ago by Hotz, Hans-Rudolf • 1.8k

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