SBML2LaTeX version 0.9.8 command-line options

Program usage

java -jar SBML2LaTeX-0.9.8_full_with_doc.jar [options]
Starts the program SBML2LATEX.
-help, -?
Lists all available options.

Input and Output Options

Configure input and output files

Here you can specify the SBML input file and the location of the LaTeX file for output.

--sbml-input-file[ |=]<File>
The SBML source file to be converted to LaTeX. Accepts sbml files (*.sbml, *.xml).
Default value: <working directory>/SBML2LaTeX/
--report-output-file[ |=]<File>
The file where to save the generated LaTeX report. The standard way is to let SBML2LaTeX generate a TeX file, which the user can then compile to a different format, or from which parts can be easily extracted to support scientific writing. Additionally, SBML2LaTeX may be used to directly generate a PDF file if the LaTeX compiler pdfLaTeX is specified. Accepts report files (*.tex, *.pdf).
Default value: <working directory>/SBML2LaTeX/
--latex-dir[ |=]<File>
Standard directory where LaTeX files can be stored Accepts directories only.
Default value: <user home>

LATEX Options

Typographical options

Here you can specify general properties such as paper size and font styles.

--font-headings[ |=]<String>
Allows to select the font of captions and other (by default sans serif) text.
All possible values for type <String> are: avant, cmss, and helvetica.
Default value: helvetica
--font-size[ |=]<Short>
This option allows you to select the size of the standard text font. Headings appear with a larger font.
All possible values for type <Short> are: 8, 9, 10, 11, 12, 14, and 17.
Default value: 11
--font-text[ |=]<String>
Allows to select the font of continuous text. Choosing 'times' is actually not recommended because in some cases equations might not look as nicely as they do when using 'mathptmx'. Default: Times font mathptmx.
All possible values for type <String> are: chancery, charter, cmr, mathptmx, palatino, times, and utopia.
Default value: mathptmx
--font-typewriter[ |=]<String>
Select a typewriter font that can be used for identifiers if option 'TYPEWRITER' is selected. URLs and other resources are also marked with this font.
All possible values for type <String> are: cmtand courier.
Default value: cmt
--paper-size[ |=]<String>
The paper size for LaTeX documents. 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.
All possible values for type <String> are: letter, legal, executive, a0, a1, a2, a3, a4, a5, a6, a7, a8, a9, b0, b1, b2, b3, b4, b5, b6, b7, b8, b9, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, d0, d1, d2, d3, d4, d5, d6, d7, d8, and d9.
Default value: a4

Specify the location of configuration files

Here you can specify the location of the SBML2LaTeX logo file and also the location of the LaTeX compiler on your operating system.

--logo-input-file[ |=]<File>
The SBML logo to be displayed at the beginning of the model report. Accepts image file (*.pdf, *.png, *.jpg).
Default value: <working directory>/SBML2LaTeX/resources/SBML2LaTeX.pdf
--load-latex-compiler[ |=]<File>
The path to the LaTeX compiler to generate PDF, DVI or other files from the created LaTeX report file. Accepts alle dateien.
Default value: <working directory>/SBML2LaTeX/

Layout options

These options allow you to influence layout and style of the LaTeX report.

--landscape[ |=]<Boolean>
This option decides whether to set the LaTeX document in landscape or portrait mode. By default most pages are in portrait format.
Default value: false
--print-names-if-available[ |=]<Boolean>
If selected, the names of SBML elements (NamedSBase) are displayed instead of their identifiers. This can only be done if the element has a name.
Default value: false
--title-page[ |=]<Boolean>
If true, a separate title page will be created. By default the title is written as a simple heading on the first page.
Default value: false
--typewriter[ |=]<Boolean>
This option decides whether a typewriter font should be applied to highlight SBML identifiers. This is particularly important when these occur in mathematical equations.
Default value: true
--reactants-overview-table[ |=]<Boolean>
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.
Default value: false

Report options

Configure the layout of the LaTeX reports, what to be included, and if to remove temporary files afterwards.

--check-consistency[ |=]<Boolean>
If true, the automatic model consistency check is performed and the results are written in the appendix of the model report file.
Default value: false
--miriam-annotation[ |=]<Boolean>
If true (default), MIRIAM annotations are included into the model report if there are any. In this case, SBML2LaTeX generates links to the resources for each annotated element. This option may require the path to the MIRIAM translation file to be specified.
Default value: true
--show-predefined-units[ |=]<Boolean>
If true (default), all predefined unit declarations of the SBML are made explicit in the report file as these are defined by the corresponding SBML Level and Version. Otherwise only unit definitions from the model are included.
Default value: true
--print-full-ode-system[ |=]<Boolean>
If set to true, the entire rate of change will be written for each species. By default, SBML2LaTeX only prints the sum of the individual reaction rates, which are hyperlinked but displayed at a different position of the report.
Default value: false
--clean-workspace[ |=]<Boolean>
If this option is set to true, all temporary files will be deleted after running SBML2LaTeX. In case of PDF creation, for instance, this will cause even the TeX file to be deleted. However, this option can be meaningful to remove all the temporary files created by your system's LaTeX compiler.
Default value: false

GUI Options

Default directories

Define the default directories to open and save files. These directories will be used as the first search target when selecting files in this graphical user interface.

--open-dir[ |=]<File>
Standard directory where user files can be found. Accepts directories only.
Default value: <working directory>/SBML2LaTeX/
--save-dir[ |=]<File>
Standard directory where the user may save some files. Accepts directories only.
Default value: <working directory>/SBML2LaTeX/

Additional options

--gui[ |=]<Boolean>
Can be used in combination with = true or = false or just --gui. Specifies whether or not a program should display its graphical user interface.
Default value: true