New protocol XML sketch idea.

new_protocols_sketch_idea.xml

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
  <!-- This is similar to the current RS protocol in Portal -->
    <protocol id="pbsmrtpipe.protocols.rs_resequencing">
        <inputs>
            <input><type>MovieFofn</type></input>
            <input><type>ReferenceEntry</type></input>
        </inputs>
        <options>
            <option id="pbsmrtpipe.task_modules.filter.my_option">
                <name>My option</name>
                <description>A description goes here</description>
                <type>int</type>
                <default>10</default>
            </option>
            <!-- more options go here -->
        </options>
    </protocol>
</workflow>

run_module_sketch.xml

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
    <!-- Run an individualy Exposed module. This is really just a group of 
    tasks that have a single interface with important options exposed -->
    <module id="pbsmrtpipe.task_modules.filter">
        <class>PB_FilterClass</class>
        <inputs>
            <input><type>MovieFofn</type></input>
        </inputs>
        <options>
            <option id="pbsmrtpipe.task_modules.filter.my_option">
                <name>My Option</name>
                <!-- etc ... -->
            </option>
        </options>
    </module>
</workflow>

run_task_sketch.xml

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
    <!-- Run a specific Task -->
    <task id="pbsmrtpipe.task_modules.filter.FilterTask">
        <inputs>
            <input><type>MovieFofn</type></input>
        </inputs>
        <options />
    </task>
</workflow>