Question: How to prevent parsing ">" into "__lt__" in Galaxy wrapper
0
gravatar for md2587
4 weeks ago by
md258710
md258710 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

ADD COMMENTlink modified 4 weeks ago by Hotz, Hans-Rudolf1.7k • written 4 weeks ago by md258710
1
gravatar for Hotz, Hans-Rudolf
4 weeks ago by
Switzerland
Hotz, Hans-Rudolf1.7k 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 COMMENTlink written 4 weeks ago by Hotz, Hans-Rudolf1.7k
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