view motif_finder.xml @ 0:95a776023fbc draft

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<tool id="eden_cluster_motif_finder" name="Motif finder" version="0.1.0">
    <description>based on EDeN</description>
    <requirements>
        <requirement type="package" version="1.6.1">biopython</requirement>
        <requirement type="package" version="13.5">eden</requirement>
    </requirements>
    <command interpreter="python">
        eden_cluster_motif_finder.py

        --input-file $infile
        --radius $radius
        --distance $distance
        --output-dir ./
        --num-nearest-neighbors $num_nearest_neighbors
        --neighborhood-intersection-size $neighborhood_intersection_size
        --fraction-center-scan $fraction_center_scan
        --output-file foo.txt
        --max-order $max_order
        --min-motif-size $min_motif_size
        --num-negative-repetitions $num_negative_repetitions
        > $output
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/>
        <param name="radius" type="integer" value="2" label="Size of the largest radius used in EDeN" help="(--radius)" />
        <param name="distance" type="integer" value="5" label="Size of the largest distance used in EDeN" help="(--distance)" />
        <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" />
        <param name="neighborhood_intersection_size" type="integer" value="5" label="Number of nearest neighbors that must be shared in neighborhood in order to trigger neighborhood joining."
            help="(--neighborhood-intersection-size)" />
        <param name="fraction_center_scan" type="float" value="1.0" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" />
        <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" />
        <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" />
        <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
    </tests>
    <help>

**What it does**

EDeN Motif finder

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**Parameters**



**References**

Fabrizio Costa

    </help>
</tool>