annotate tools/myTools/6_sfa_perts.xml @ 1:7e5c71b2e71f draft default tip

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<tool id="netisce6" name="Netisce Step 6" version="0.1.0" python_template_version="3.5">
<description>Computes the attractors from perturbations on FVS control nodes</description>

    <requirements>
        <requirement type="package" version="1.19.5">numpy</requirement>
        <requirement type="package" version="1.1.5">pandas</requirement>
        <requirement type="package" version="3.5.0">os</requirement>
        <requirement type="package" version="1.11.0">networkx</requirement>
        <requirement type="package" version="3.5.0">random</requirement>
        <requirement type="package" version="3.1.14">sfa</requirement>
        <requirement type="package" version="1.0.1">sklearn.preprocessing</requirement>
        <requirement type="package" version="3.5.0">csv</requirement>
        <requirement type="package" version="3.5.0">sys</requirement>
    </requirements>

    <command>python3 '$__tool_directory__/bin/SFA_virtscreen.py' '$network' '$expression_data' '$init' '$samples' '$fvs' '$fvs_init'</command>

    <inputs>
        <param name="network" type="data" format="sif" label="Network"/>
        <param name="expression_data" type="data" format="csv" label="Expression Data"/>
        <param name="init" type="text" value="resistant" label="Name of Undesired Initial State"/>
        <param name="samples" type="data" format="txt" label="Names of all Experimental Samples"/>
        <param name="fvs" type="data" format="txt" label="Minimal Feedback Vertex Set"/>
        <param name="fvs_init" type="data" format="txt" label="Perturbations of the FVS Set"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular" from_work_dir="pert_logss.txt" label="Attractors when the FVS Set is randomly perturbed"/>
    </outputs>

    <tests>
        <test>
            <param name="network" value="network.sif" />
            <param name="expression_data" value="expressions.csv" />
            <param name="init" value="resistant" />
            <param name="samples" value="samples.txt" />
            <param name="fvs" value="fvs.txt"/>
            <param name="fvs_init" value="init.txt" />
            <output name="output" value="pert_logss.tsv" ftype="tsv" />
        </test>
    </tests>

    <help>
    This tool computes Computes the attractors from perturbations on FVS control nodes. 
    Required Inputs:
    1. network in sif format (activating edges as "activates", inhibitory edges as "inhibits")
    2. normalized expression values for data sample (rows are expressed genes, columns are samples)
    3. name of undesired initial state/experimental sample
    4. name of all experimental samples of interest
    5. minimal Feedback Vertex set of the network
    6. randomly generated perturbations of FVS Set
    </help>

    <citations>
        <citation type="doi">10.1038/s41598-019-50790-0</citation>
    </citations>

</tool>