annotate inchlib_clust/inchlib_clust.xml @ 0:60f93f839759 draft default tip

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<tool id="inchlib_clust" name="INCHlib" version="1.0.0" hidden="false">
    <requirements>
        <requirement type="package" version="3.5.0">blas</requirement>
        <requirement type="package" version="1.7">numpy</requirement>
        <requirement type="package" version="0.12">scipy</requirement>
        <requirement type="package" version="0.15">scikit-learn</requirement>
        <requirement type="package" version="1.1.13">fastcluster</requirement>
        <requirement type="python-module">numpy</requirement>
        <requirement type="python-module">scipy</requirement>
        <requirement type="python-module">scikit-learn</requirement>
        <requirement type="python-module">fastcluster</requirement>
    </requirements>
    <description>Performs data clustering for input to InCHlib.js</description>
    <command interpreter="python">
        inchlib_clust.py $input -o $output
                        --row_distance $row_distance
                        --row_linkage $row_linkage
                        --column_distance $column_distance
                        --column_linkage $column_linkage
                        --axis $axis
                        --datatype $datatype
                        --data_delimiter $data_delimiter
                    #if $data_header.data_header_present == "yes"
                        --data_header
                    #end if
                    #if $metadata_option.metadata_present == "yes"
                        --metadata $metadata_option.metadata
                        --metadata_delimiter $metadata_option.metadata_delimiter
                        #if $metadata_option.metadata_header.metadata_header_present == "yes"
                            --metadata_header
                        #end if
                        #if $metadata_option.metadata_compress_option.should_compress_metadata == "yes"
                            --metadata_compressed_value $metadata_option.metadata_compressed_value
                        #end if
                        #end if
                    #if $data_compress_option.should_compress_data == "yes"
                        --data_compressed_value $data_compressed_value
                    #end if
                    #if $should_normalize == "yes"
                        --normalize
                    #end if
    </command>
    <inputs>
        <param format="text" name="input" type="data" label="Input File" />

        <param name="row_distance" type="select" label="Row Distance Method" help="Set the distance to use for clustering rows">
            <option value="braycurtis">braycurtis</option>
            <option value="canberra">canberra</option>
            <option value="chebyshev">chebyshev</option>
            <option value="cityblock">cityblock</option>
            <option value="correlation">correlation</option>
            <option value="cosine">cosine</option>
            <option value="euclidean" selected="true">euclidean</option>
            <option value="mahalanobis">mahalanobis</option>
            <option value="minkowski">minkowski</option>
            <option value="seuclidean">seuclidean</option>
            <option value="sqeuclidean">sqeuclidean</option>

            <option value="dice">dice</option>
            <option value="hamming">hamming</option>
            <option value="jaccard">jaccard</option>
            <option value="kulsinski">kulsinski</option>
            <option value="matching">matching</option>
            <option value="rogerstanimoto">rogerstanimoto</option>
            <option value="russellrao">russellrao</option>
            <option value="sokalmichener">sokalmichener</option>
            <option value="sokalsneath">sokalsneath</option>
            <option value="yule">yule</option>
        </param>

        <param name="row_linkage" type="select" label="Row Linkage Method" help="Set the linkage to use for clustering rows">
                <option value="single">single</option>
                <option value="complete">complete</option>
                <option value="average">average</option>
                <option value="centroid">centroid</option>
                <option value="ward">ward</option>
                <option value="median">median</option>
                <option value="weighted">weighted</option>

                <option value="ward" selected="true">ward</option>
                <option value="centroid">centroid</option>
        </param>

        <param name="column_distance" type="select" label="Column Distance Method" help="Set the distance to use for clustering columns">
            <option value="braycurtis">braycurtis</option>
            <option value="canberra">canberra</option>
            <option value="chebyshev">chebyshev</option>
            <option value="cityblock">cityblock</option>
            <option value="correlation">correlation</option>
            <option value="cosine">cosine</option>
            <option value="euclidean" selected="true">euclidean</option>
            <option value="mahalanobis">mahalanobis</option>
            <option value="minkowski">minkowski</option>
            <option value="seuclidean">seuclidean</option>
            <option value="sqeuclidean">sqeuclidean</option>

            <option value="dice">dice</option>
            <option value="hamming">hamming</option>
            <option value="jaccard">jaccard</option>
            <option value="kulsinski">kulsinski</option>
            <option value="matching">matching</option>
            <option value="rogerstanimoto">rogerstanimoto</option>
            <option value="russellrao">russellrao</option>
            <option value="sokalmichener">sokalmichener</option>
            <option value="sokalsneath">sokalsneath</option>
            <option value="yule">yule</option>
        </param>

        <param name="column_linkage" type="select" label="Column Linkage" help="Set the linkage to use for clustering columns">
                <option value="single">single</option>
                <option value="complete">complete</option>
                <option value="average">average</option>
                <option value="centroid">centroid</option>
                <option value="ward">ward</option>
                <option value="median">median</option>
                <option value="weighted">weighted</option>

                <option value="ward" selected="true">ward</option>
                <option value="centroid">centroid</option>
        </param>

        <param name="axis" type="select" label="Clustering Axis">
            <option value="row" selected="true">row</option>
            <option value="both">both</option>
        </param>

        <param name="datatype" type="select" label="Type Of Data">
            <option value="numeric" selected="true">numeric</option>
            <option value="binary">binary</option>
        </param>

        <param name="data_delimiter" type="select" label="Data Delimiter">
            <option value="\t">tab</option>
            <option value=",">comma</option>
            <option value=";">semicolon</option>
        </param>

        <conditional name="data_header">
            <param name="data_header_present" type="select" label="First row of file is header">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
        </conditional>

        <conditional name="data_compress_option">
            <param name="should_compress_data" type="select" label="Compress Rows">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="data_compressed_value" type="select">
                    <option value="median" selected="true">median</option>
                    <option value="mean">mean</option>
                </param>
            </when>
        </conditional>

        <param name="should_normalize" type="select" label="Normalise">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
        </param>

        <conditional name="metadata_option">
            <param name="metadata_present" type="select" label="Metadata Input">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="metadata" type="data" format="text" label="Metadata File"/>
                <conditional name="metadata_header">
                    <param name="metadata_header_present" type="select" label="Metadata Header Present?">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                </conditional>
                <param name="metadata_delimiter" type="select" label="Metadata Delimiter">
                    <option value="\t">tab</option>
                    <option value=",">comma</option>
                    <option value=";">semicolon</option>
                </param>
                <conditional name="metadata_compress_option">
                    <param name="should_compress_metadata" type="select" label="Compress Metadata Rows?">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="metadata_compressed_value" type="select">
                            <option value="median" selected="true">median</option>
                            <option value="mean">mean</option>
                            <option value="frequency">frequency</option>
                        </param>
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="json" name="output" label="${tool.name} on ${on_string}: output" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="inchlib_input1.csv"/>
            <param name="row_distance" value="euclidean"/>
            <param name="row_linkage" value="ward"/>
            <param name="column_distance" value="euclidean"/>
            <param name="column_linkage" value="ward"/>
            <param name="axis" value="row" />
            <param name="datatype" value="numeric" />
            <param name="data_delimiter" value="," />
            <param name="data_header_present" value="yes" />
            <param name="should_compress_data" value="no" />
            <param name="should_normalize" value="no" />
            <param name="metadata_present" value="yes" />
            <param name="metadata" value="inchlib_input_metadata.csv" />
            <param name="metadata_delimiter" value="," />
            <param name="metadata_header_present" value="yes" />
            <output name="output" file="inchlib_output.json" ftype="json" />
        </test>
    </tests>

    <help>
        **What it does**

            Performs data clustering and prepares input data for InCHlib.


    </help>
</tool>