Galaxy wrappers for common unix text-processing tools

NOTE About Security

The included tools are secure (barring unintentional bugs): The main concern might be executing system commands with awk's "system" and sed's "e" commands, or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands. These commands are DISABLED using the "--sandbox" parameter to awk and sed.

User trying to run an awk program similar to:

BEGIN { system("ls") }

Will get an error (in Galaxy) saying:

fatal: 'system' function not allowed in sandbox mode.

User trying to run a SED program similar to:

1els

will get an error (in Galaxy) saying:

sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode

That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them.

Installation

Should be done via the Galaxy Tool Shed. Install the following repository: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing

TODO

• add shuf, we can remove the random feature from sort and use shuf instead
• move some advanced settings under a conditional, for example the cut tools offers to cut bytes
• cut wrapper has some output conditional magic for interval files, that needs to be checked
• comm wrapper, see the Galaxy default one
• evaluate the join wrappers against the Galaxy ones, maybe we should drop them

License

• Copyright (c) 2009-2013 A. Gordon (gordon <at> cshl dot edu)
• Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening <at> gmail dot com)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.