.. _command_line_tool_index:

Command Line Tool Index
=======================

.. toctree::
   :maxdepth: 1
   :caption: Setting up and running a simulation:

    w_init       <command_line_tools/w_init>
    w_bins       <command_line_tools/w_bins>
    w_run        <command_line_tools/w_run>
    w_truncate   <command_line_tools/w_truncate>
    w_fork       <command_line_tools/w_fork>



.. toctree::
   :maxdepth: 1
   :caption: Analyzing a simulation:

    w_assign     <command_line_tools/w_assign>
    w_trace      <command_line_tools/w_trace>
    w_fluxanl    <command_line_tools/w_fluxanl>
    w_ipa        <command_line_tools/w_ipa>
    w_pdist      <command_line_tools/w_pdist>
    w_succ       <command_line_tools/w_succ>
    w_crawl      <command_line_tools/w_crawl>
    w_direct     <command_line_tools/w_direct>
    w_select     <command_line_tools/w_select>
    w_states     <command_line_tools/w_states>
    w_eddist     <command_line_tools/w_eddist>
    w_ntop       <command_line_tools/w_ntop>


.. toctree::
   :maxdepth: 1
   :caption: Plotting tools:

    plothist     <command_line_tools/plothist>
    ploterr      <command_line_tools/ploterr>


.. toctree::
   :maxdepth: 1
   :caption: Deprecated tools:

    w_kinavg     <command_line_tools/w_kinavg>
    w_kinetics   <command_line_tools/w_kinetics>
    w_stateprobs <command_line_tools/w_stateprobs>