view EDeN_nearest_neighbor.xml @ 7:59b3b6ce10bb draft

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<tool id="bg_eden_nearest_neighbor" name="EDeN Nearest Neighbors" version="0.1">
    <description></description>
    <expand macro="requirements" />
    <macros>
        <import>eden_macros.xml</import>
    </macros>
    <command>
        tmp_dir=`mktemp -d -u`;
        EDeN --action NEAREST_NEIGHBOR

        --input_data_file_name $infile
        --target_file_name $target_infile

        --file_type "SPARSE_VECTOR"
        --binary_file_type

        @kernel_type_options@
        --graph_type $graph_type
        @input_smooth_conditional@

        @normalization_kernel_hash_radius_dist_vertex@

        --output_directory_path \$tmp_dir


        ##
        ## shuffling files to create the correct outputs for Galaxy
        ##

        ;
        cp \$tmp_dir/knn $ofile_nnlist 2> /dev/null
        
        ## Nearest neighbor feature representation
        #if 'nnf' in str($additional_outputs).split(','):
            ;
            cp \$tmp_dir/knn_feature $ofile_nnf 2> /dev/null
        #end if

        ## Nearest neighbor target value list
        #if 'nnt' in str($additional_outputs).split(','):
            ;
            cp \$tmp_dir/knn_target_value $ofile_nnt 2> /dev/null
        #end if

        ## Nearest neighbor kernel value list
        #if 'nnk' in str($additional_outputs).split(','):
            ;
            cp \$tmp_dir/knn_kernel_value $ofile_nnk 2> /dev/null
        #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" />

        <expand macro="kernel_type_options" />

        <expand macro="graph_types" />

        <expand macro="normalization_kernel_hash_radius_dist_vertex" />

        <param name="additional_outputs" type="select" multiple="true" optional="True" label="Additional outputs">
            <option value="none" selected="True">No additional output</option>
            <option value="nnk">Nearest neighbor kernel value list</option>
            <option value="nnt">Nearest neighbor target value list</option>
            <option value="nnf">Nearest neighbor feature representation</option>
        </param>

    </inputs>
    <outputs>
        <data format="tabular" name="ofile_nnlist" label="${tool.name} on ${on_string}"/>
        <data format="tabular" name="ofile_nnf" label="${tool.name} on ${on_string} (Nearest neighbor feature representation)">
          <filter>'nnf' in additional_outputs</filter>
        </data>
        <data format="tabular" name="ofile_nnt" label="${tool.name} on ${on_string} (Nearest neighbor target value list)">
          <filter>'nnt' in additional_outputs</filter>
        </data>
        <data format="tabular" name="ofile_nnk" label="${tool.name} on ${on_string} (Nearest neighbor kernel value list)">
          <filter>'nnk' in additional_outputs</filter>
        </data>
    </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.

@references@

    </help>
</tool>