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Language: Shell Script
Summary Reformat an SBML file
Author(s) Bruce E. Shapiro,
Michael Hucka
Version 2010-04-23
Needs tidy vers. of 2009 or later
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Link for copying


This simple script invokes the program tidy (available for Unix-like systems such as Linux and MacOS X) to reformat an XML SBML file. It writes the pretty-printed result to a destination file. This wrapper simplifies the task of invoking tidy on SBML files by supplying some preselected arguments, so that users don't need to worry about it—users can just invoke sbmltidy on an SBML file and be done with it.

Installation instructions

  1. Install a recent (at least March 2009) version of the tidy program and make sure it is accessible on your shell's command search $path.
  2. Copy to a location on your computer's hard disk.
  3. Make sure is accessible on your shell's command search $path, or else invoke using the full path to its location.

Usage input.xml output.xml

The input.xml file is the file that you want to reformat; the output.xml is the desired destination where the formatted output should be written. Both the input file and the destination output files must be specified on the command line. If the destination file exists, it will be overwritten.

Known problems/issues

The XML formatting produced by this utility does not match what libSBML produces, although there are substantial similarities. Probably the most noticeable difference is that sbmltidy puts each attribute-value pair of an element on a separate line. Depending on your tastes, you may prefer one or the other style of XML formatting.

Licensing terms and distribution

This program is in the public domain.

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This page was last modified 21:57, 23 April 2010.

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