comparison tools/myTools/12_extract_perts.xml @ 1:7e5c71b2e71f draft default tip

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<tool id="netisce12" name="Netisce Step 12" version="0.1.0" python_template_version="3.5">
<description>Extracts the combinations of perturbations on FVS control nodes that pass filtering criterion 2</description>

    <requirements>
        <requirement type="package" version="1.1.5">pandas</requirement>
        <requirement type="package" version="3.5.0">sys</requirement>
    </requirements>
    
    <command> python3 '$__tool_directory__/bin/get_perts.py' '$fvs_init' '$fvs' '$filtered_perts' </command>

    <inputs>
        <param name="fvs_init" type="data" format="txt" label="FVS perturbations initialization"/>
        <param name="fvs" type="data" format="txt" label="Minimal Feedback Vertex Set"/>
        <param name="filtered_perts" type="data" format="txt" label="list of perturbation IDs that passed filtering criterion 2. "/>

    </inputs>

    <outputs>
        <data name="output" format="txt" from_work_dir="extracted_perts.txt" label="combinations of perturbations on FVS control nodes that pass filtering criterion 2."/>
    </outputs>

    <tests>
        <test>
            <param name="fvs_init" value="init.txt"/>
            <param name="fvs" value="fvs.txt"/>
            <param name="filtered_perts" value="crit2_perturbations.txt"/>
            <output name="output" value="extract_perts.txt" ftype="txt" />
        </test>
    </tests>

    <help>
    This tool extracts the combinations of perturbations on FVS control nodes that pass filtering criterion 2.
    Required Inputs:
    1. Random Perturbation States for Feedback Vertex Set
    2. Feedback Vertex Set
    3. Perturbation Attractors that successfully shifted the network from undesired to desired state
    </help>

</tool>