SBML2LATEX command line arguments

This page gives you an overview of the command line argumenst of SBML2LATEX up to version 0.9.7.

Usage

java [-cp <classpath definition>] SBMLconverter [in_file.xml] [out_file.tex] [options]

Note that it is probably necessary to set the environment variable LD_LIBRARY_PATH to the location of libSBML together with its XML parser library before calling SBMLconverter.

Usage of the script displaySBML.sh

displaySBML.sh in_file.xml [tex|latex|pdf|ps|eps|dvi|jpg|png|gif] [options]

This script accepts the same options as SBMLconverter itself. Note that it is, however, probably necessary to customize this shell script because some paths within the script may not point to the correct locations on your system. It is also important to know that this script requires LATEX, ImageMagick and ZIP to be installed on your system in addition to all requirements of SBML2LATEX itself. For details see the download section.

Possible command line options (case and ordering are ignored)

1. Options to include or exclude SBML information

--show-predefined-units=<true|false>
If true (default), all predefined unit definitions of SBML are made explicit.
--miriam=<true|false>
If true (default), MIRIAM annotations are included into the model report if there are any. This option may require the path to the MIRIAM translation file to be specified.
--check-consistency=<true|false>
If true, the libSBML model consistency check is performed and the results are written in the glossary of the model report.

2. Layout options for the model report

--paper-size=<a<0..9>|b<0..9>|c<0..9>|d<0..9>|letter|legal|executive>
With this option the paper format can be influenced. Default paper size: DIN A4. All sizes a?, b?, c? and d? are European DIN sizes. Letter, legal and executive are US paper formats.
--landscape=<true|false>
If true, the whole report is written on landscape paper instead of portrait format.
--title-page=<true|false>
If true, an extra title page will be created.
--font-size=<8|9|10|11|12|14|17>
This option allows you to select a smaller or larger font (for continuous text). Default size: 11 pt.
--font-text=<chancery|charter|cmr|palatino|times|utopia>
Allows to select the font of continuous text. Default: times.
--font-headings=<avant|cmss|helvetica>
Allows to select the font of captions and other sans serif text. Default: helvetica
--typewriter=<true|false>
If true (default) all identifiers are written in typewriter font.
--font-typewriter=<cmt|courier>
Selects the font to be used for typewriter text. Default: cmt.
--print-name-if-available=<true|false>
If true, the names of elements are used in equations instead of their identifiers.
--reactants-overview-table=<true|false>
If true, the details (identifier and name) of all reactants, modifiers and products participating in a reaction are listed in one table. By default a separate table is created for each one of the three participant groups including its SBO term.

3. Definition of required file paths

--logo-file=<path to logo file (a graphics file)>
The SBML logo to be displayed at the beginning of the model report. Default path: resources/SBML2LaTeX.pdf
--sbo-file=<path to SBO obo file>
The file containing the SBO translation in OBO format. Default path: resources/SBO_OBO.obo
--miriam-file=<path to MIRIAM XML file>
The file containing the translation of URNs/URIs to actual URLs. Default path: resources/MIRIAM.xml
--html-config-file=<path to HTML2LATEX configuration file>
The configuration file for the translation of notes in XHTML format to LATEX commands and text. Default path: resources/config.xml

4. General program options

--gui
Opens a dialog window for convenient usage. With this option no in/out-file needs to be specified. All other command line options are accepted and their values influence the behavior of the dialog window. See the following screenshot
--help
Shows this overview.