view EDeN_nearest_neighbor.xml @ 6:7d49e315cb95 draft

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<tool id="bg_eden_nearest_neighbor" name="EDeN Nearest Neighbors" version="0.1">
    <description></description>
    <requirements>
    </requirements>
    <macros>
        <import>eden_macros.xml</import>
    </macros>
    <command>
        EDeN --action NEAREST_NEIGHBOR

        --input_data_file_name $infile
        --target_file_name $target_infile

        --file_type "SPARSE_VECTOR"
        --binary_file_type

        ### Adds rescaled features from nearest neighbors ###

        #if $smooth_opts.smooth_opts_selector == 'smooth':
            --smooth
            --smooth_param $smooth_opts.smoother_param

            --row_index_file_name $row_index_file_name
            --col_index_file_name $col_index_file_name
            --num_hash_functions $smooth_opts.num_hash_functions
            --num_repeat_hash_functions $smooth_opts.num_repeat_hash_functions
            --max_size_bin $smooth_opts.max_size_bin
            --eccess_neighbour_size_factor $smooth_opts.eccess_neighbour_size_factor
            --num_nearest_neighbours $smooth_opts.num_nearest_neighbours
            $smooth_opts.shared_neighborhood
            $smooth_opts.no_neighborhood_cache
            $smooth_opts.no_minhash_cache
        #end if

    </command>
    <inputs>

        <param format="eden_sparse_vector" name="infile" type="data" label="Input Graph" help=""/>
        <param format="txt" name="target_infile" type="data" label="Target file" help=""/>

        <expand macro="input_smooth_conditional" />

    </inputs>
    <outputs>
        <data format="gspan" name="outfile" label="gSpan from ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="3_molceuls.sdf" />
            <output name="outfile" file="3_molecules.gspan" />
        </test>
    </tests>
    <help>

.. class:: infomark

**What it does** 

Nearest neighbors are efficiently identified with a locality sensitive hashing technique.

This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa.

    </help>
</tool>