Here are the commands that are currently supported that can be included in the script file:

    * open sessionfile
          o Open a session file
    * import [network|node attributes|edge attribute] filename
          o Import a network or attribute data
    * layout layout-algorithm tunable1=value1 tunable2=value2 etc.
          o Layout the network using the layout layout-algorithm with the tunables set to the appropriate values
    * export [vizmap|node attributes|edge attributes] to filename
          o Export the vizmap and node or edge attributes to a file
    * export network as [XGMML, PSI-MI, GML, SIF, PDF, SVG, PNG, GIF, JPG] to filename
          o Export a network as either a network data file or a graphics file
    * save as filename
          o Save a Cytoscape session file
    * apply vizmap
          o Apply vizmap map vizmap to the current network
    * exit
          o Exit Cytoscape

Example (test.com):

    import network pte.xgmml
    import node attributes subgroup.noa
    layout force-directed
    export network as pdf to test.pdf zoom=10
    exit

You can execute this file by executing Cytoscape with the "-S" flag:

    cytoscape.sh -S test.com


Here are the tunables for some of the cytoscape layouts:

force-directed (Force Directed):
>
>      "defaultSpringCoefficient", "Default Spring Coefficient"
>      "defaultSpringLength", "Default Spring Length"
>      "defaultNodeMass", "Default Node Mass"
>      "numIterations", "Number of Iterations"
>      "min_weight", "The minimum edge weight to consider"
>      "max_weight", "The maximum edge weight to consider"
>      "integrator", "Integration algorithm to use"
>      "selected_only", "Only layout selected nodes"
>      "edge_attribute", "The edge attribute that contains the weights"
>
>
>  fruchterman-rheingold (Biolayout):
>
>      "partition", "Partition graph before layout"
>      "randomize", "Randomize graph before layout"
>      "min_weight", "The minimum edge weight to consider"
>      "max_weight", "The maximum edge weight to consider"
>      "selected_only", "Only layout selected nodes"
>      "edge_attribute", "The edge attribute that contains the weights"
>      "repulsion_multiplier", "Multiplier to calculate the repulsion force"
>      "attraction_multiplier", "Divisor to calculate the attraction force"
>      "gravity_multiplier", "Multiplier to calculate the gravity force"
>      "iterations", "Number of iterations"
>      "temperature", "Initial temperature"
>      "spread_factor", "Amount of extra room for layout"
>      "update_iterations", "Number of iterations before updating display"
>      "conflict_avoidance", "Constant force applied to avoid conflicts"
>      "max_distance_factor", "Percent of graph used for node repulsion calculations"
>
>  kamada-kawaii (Spring Embedded:
>
>      "partition", "Partition graph before layout"
>      "randomize", "Randomize graph before layout"
>      "min_weight", "The minimum edge weight to consider"
>      "max_weight", "The maximum edge weight to consider"
>      "selected_only", "Only layout selected nodes"
>      "edge_attribute", "The edge attribute that contains the weights"
>      "iterations_pernode", "Number of iteratations for each node"
>      "layout_passes", "Number of layout passes"
>      "distance_strength", "Spring strength"
>      "rest_length", "Spring rest length"
>      "disconnected_strength", "Strength of a 'disconnected' spring"
>      "disconnected_rest_length", "Rest length of a 'disconnected' spring"
>      "anticollisionStrength", "Strength to apply to avoid collisions"