Tasks XML Manifest

abstract_graph_example.xml

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
    <!-- Not sure this make sense to be here -->
    <settings>
        <param id="pbsmrtpipe.task_modules.filter.my_option">
            <value>12</value>
        </param>
    </settings>
    <abstract-graph id="pbsmrtpipe.abstract_graphs.rs_resequencing">
        <file-node id="2">
            <file id="pbsmrtpipe.resource_types.FastaType" />
        </file-node>
        <file-node id="2">
            <file id="pbsmrtpipe.resource_types.MovieFofn" />
        </file-node>
        <task-node id="1234">
            <task id="pbsmrtpipe.task_modules.filter.FilterTask" />
            <inputs>
                <!-- This encode the bindings -->
                <file-node id="1"/>
                <file-node id="2" />
            </inputs>
            <outputs>
                <file-node id="3" />
            </outputs>
        </task-node>
    </abstract-graph>
</workflow>

tasks_manifest.xml

<?xml version="1.0" encoding="UTF-8"?>
<tasks>
    <!-- Manifests of all tasks. This can be created by intraspection of the tasks defined in pbsmrtpipe.task_modules.* -->
    <task id="pbsmrtpipe.task_modules.filter.FilterTask">
        <!-- Type Signature of the constructor Task Positionally -->
        <input-types>
            <file-type id="pbsmrtpipe.resource_types.MovieFofn" />
            <file-type id="pbsmrtpipe.resource_types.FastaFile" />
        </input-types>
        <output-type>
            <file-type id="pbsmrptipe.resource_types.FilteredRegionsFofn"/>
        </output-type>
        <options>
            <option id="my_option">
                <!-- The id maps the type class and can be more involved. IntRange(1, 100) -->
                <type id="Int" />
                <default>12</default>
                <optional>False</optional>
            </option>
        </options>
    </task>
    <!-- Mapping Task -->
    <!-- SubreadFiltering etc.. -->
</tasks>

workflow_preset.xml

<?xml version="1.0" encoding="UTF-8"?>
<presets>
    <workflow id="rs_resequencing">
        <!-- A preset is specifc settings + an abstract graph id -->
        <abstract-graph id="pbsmrtpipe.abstract_graphs.rs_resequencing"/>
        <inputs>
            <file id="pbsmrtpipe.resource_types.MovieFofn" />
            <file id="pbsmrptipe.rosource_types.ReferenceEntry">
                <default>/path/to/common/references/ecoli_dir</default>
            </file>
        </inputs>
        <settings>
            <param id="pbsmrtpipe.task_modules.filter.my_option">
                <name> My Option</name>
                <value>12</value>
                <hidden>False</hidden>
            </param>
        </settings>
    </workflow>
    <workflow id="rs_resequencing_with_control">
        <abstract-graph id="pbsmrtpipe.abstract_graphs.rs_control_resequencing"/>
        <settings>
            <param id="pbsmrtpipe.task_modules.filter.my_option">
                <name> My Option</name>
                <value>12</value>
                <hidden>False</hidden>
            </param>
        </settings>
    </workflow>
</presets>