---
title: Command Line
noheader: true
permalink: cli_documentation/
layout: documentation
location: cli_documentation

---


<p>wot provides a command line interface that offers fine-grained control over calculations.
    <br>
    Help is available for each tool using the syntax <span class="text-monospace">wot tool -h</span>. For example, <span
            class="text-monospace">wot optimal_transport -h</span>. We recommend
    <a href="https://pegasus.readthedocs.io/en/latest/">pegasus</a> for preprocessing, visualization, and clustering
    tools.
</p>

<hr/>
{% for tool in site.data.tools %}
<div style="border-bottom: 1px solid rgba(0,0,0,.125);padding-bottom: 14px;">
    <h2>{{ tool.name }}</h2>

    <a data-toggle="collapse" href="#{{ tool.name }}_details" role="button"
       aria-expanded="false" aria-controls="{{ tool.name }}_details">
        {{ tool.desc }}
    </a>
    <div style="margin-left: 14px;" id="{{ tool.name }}_details" class="collapse">
        <table class="table table-sm">
            <tr>
                <th>Parameter</th>
                <th>Description</th>
            </tr>
            {% for param in tool.params %}
            <tr>

                <td>{% if param.required %} <b> {% endif %} {{param.name}} {% if param.required %} </b> {% endif %}
                </td>
                <td>{{param.help}}{% if param.choices %}<br/>Choices: {{param.choices | join: ", "}} {% endif %}{% if
                    param.default %}<br/>Default: {{param.default}} {% endif %}
                </td>
            </tr>
            {% endfor %}
        </table>
        {% if site.data.examples[tool.name] %}
        <b>Example Usage:</b><br/>
        <span class="text-monospace">wot {{tool.name }} {{ site.data.examples[tool.name].code }}</span><br/>
        {{ site.data.examples[tool.name].text }}
        {% endif %}
    </div>
</div>
{% endfor %}




