annotate 2d_feature_extraction.xml @ 6:5bc8cdc17fd0 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c86a1b93cb7732f7331a981d13465653cc1a2790

<tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with scikit-image</description>
    <macros>
        <import>creators.xml</import>
        <token name="@TOOL_VERSION@">0.18.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">scikit-image</xref>
        <xref type="biii">scikit-image</xref>
    </xrefs>
    <requirements> 
        <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
        <requirement type="package" version="2.2.2">pandas</requirement>
        <requirement type="package" version="1.23.3">numpy</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
        <requirement type="package" version="0.1">giatools</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
    python '$__tool_directory__/2d_feature_extraction.py'
    #if $feature_options['features'] == 'all'
      --all
    #else if $feature_options['features'] == 'select'
      ${' '.join(str( $feature_options['selected_features'] ).split(','))}
    #end if
    #if $use_raw_option['use_raw'] == 'raw_image'
      --raw '$input_raw'
    #end if
    '$input_label' '$output'
    ]]>
    </command>
    <inputs>
        <param name="input_label" type="data" format="tiff,png" label="Label map" />
        <conditional name="use_raw_option">
            <param label="Use the intensity image to compute additional features" name="use_raw" type="select">
                <option selected="True" value="no_original">No intensity image</option>
                <option value="raw_image">Use intensity image</option>
            </param>
            <when value="no_original"></when>
            <when value="raw_image">
                <param name="input_raw" type="data" format="tiff,png" label="Intensity image" />
            </when>
        </conditional>
        <conditional name="feature_options">
            <param label="Select features to compute" name="features" type="select">
                <option selected="True" value="all">All features</option>
                <option value="select">Select features</option>
            </param>
            <when value="all"> </when>
            <when value="select">
                <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
                    <option value="--label">Label from the label map</option>
                    <option value="--patches">Patches (requires original image)</option>
                    <option value="--max_intensity">Max Intensity (requires original image)</option>
                    <option value="--mean_intensity">Mean Intensity (requires original image)</option>
                    <option value="--min_intensity">Minimum Intensity (requires original image)</option>
                    <option value="--moments_hu">Moments Hu</option>
                    <option value="--centroid">Centroid</option>
                    <option value="--bbox">Bounding box</option>
                    <option value="--area">Area</option>
                    <option value="--filled_area">Filled area</option>
                    <option value="--convex_area">Convex area</option>
                    <option value="--perimeter">Perimeter</option>
                    <option value="--extent">Extent</option>
                    <option value="--eccentricity">Eccentricity</option>
                    <option value="--equivalent_diameter">Equivalent diameter</option>
                    <option value="--euler_number">Euler number</option>
                    <option value="--inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
                    <option value="--major_axis_length">Major axis length</option>
                    <option value="--minor_axis_length">Minor axis length</option>
                    <option value="--orientation">Orientation</option>
                    <option value="--solidity">Solidity</option>
                    <option value="--moments">Moments</option>
                    <option value="--convexity">Convexity</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
       <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input_label" value="input.tiff"/>
            <param name="features" value="select"/>
            <param name="selected_features" value="--label,--area"/>
            <output name="output" ftype="tabular" value="out.tsv"/>
        </test>
    </tests>
    <help>

        **Computes features of a label map.**

        The computed features are computed based solely on the properties of the labels in the label map,
        or, optionally, by also taking the intensities from a corresponding intensity image into account.

        The label map must be a 2-D or 3-D single-channel image.
    
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>