Mercurial > repos > bjoern-gruening > sed_wrapper
changeset 0:e850a63e5aed
initial uploaded
| author | bjoern-gruening |
|---|---|
| date | Thu, 15 Mar 2012 04:53:54 -0400 |
| parents | |
| children | 12ac67b5c81d |
| files | readme.txt sed.xml tool_conf.xml |
| diffstat | 3 files changed, 120 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Thu Mar 15 04:53:54 2012 -0400 @@ -0,0 +1,67 @@ +Galaxy wrapper for sed +====================== + +This wrapper is copyright 2012 by Björn Grüning. + +This is a wrapper for the sed command line tool. + +sed is a stream editor included in every unix-derived operating system. +That wrapper only uses a small subset of the sed functionality. Its only a wrapper for: + +sed -r '$pattern' $input + + +WARNING: +======== + +No syntax check and sanitising will happen in that wrapper. This wrapper may harm your computer ;) +Nevertheless, i think it can be useable for some installations. + + +Installation +============ + +sed should be available on every unix derived operating system and belongs to the classical unix programms. +No further installation is requiered. + +For more information have a look at the following pages: + +http://en.wikipedia.org/wiki/Sed +http://www.gnu.org/software/sed/manual/sed.html + +To install the wrapper copy the sed folder in the galaxy tools +folder and modify the tools_conf.xml file to make the tool available to Galaxy. +For example: + +<toolbox> + <tool file="text_manipulation/sed.xml" /> +</toolbox> + + +History +======= + +v0.1 - Initial public release + + +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sed.xml Thu Mar 15 04:53:54 2012 -0400 @@ -0,0 +1,49 @@ +<tool id="sed_stream_editor" name="Manipulation" version="0.0.1"> + <description>of text lines with regular expressions (sed)</description> + <command>sed -r '$pattern' $input > $outfile</command> + <inputs> + <param format="txt, tabular" name="input" type="data" label="Replace lines from"/> + <param name="pattern" size="40" type="text" value="" label="the pattern" help="here you can enter your sed expression (No syntax check or sanitising!)" /> + </inputs> + <outputs> + <data format="input" name="outfile" metadata_source="input"/> + </outputs> + <options sanitize="False"/> + <requirements> + <requirement type="binary">sed</requirement> + </requirements> + <tests> + + </tests> + <help> + +.. class:: warningmark + +Use with caution! Its a plain wrapper around **sed** and the input is not sanitized. + + +----- + +**What it does** + +Changes every line of a text file according to a given regular expression. + +----- + +**Syntax** + +Use the **sed**-syntax -> **s/find-pattern/replace-pattern/** + +**Example** + +- **s/x/-/** Replace all **x** with **-**. + +- **s/_.*//** Splits a string after **_** and replaces the rest with nothing. +- **s/[^_]*_*//** Splits a string after **_** and replaces the first part with nothing. + +- **s/\\s.*//** Splits a string after whitespaces and replaces the rest with nothing. +- **s/\\S*\\s*//** Splits a string after whitespaces and replaces the first part with nothing. + + +</help> +</tool>