comparison enhance_or_suppress_features.xml @ 6:bace5a93a97c draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

5:11f177b1a59e

<tool id="cp_enhance_or_suppress_features" name="EnhanceOrSuppressFeatures" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>to improve subsequent identification of objects</description>

    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="feature_speckles">
            <param name="speckles_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size." />
            <param name="speed_accuracy" label="Speed and accuracy" type="select">
                <help>
                    <![CDATA[

            <param name="dic_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" help="Specifies the amount of smoothing of the image in the direction parallel to the shear axis of the image. The line integration method will leave streaks in the image without smoothing as it encounters noisy pixels during the course of the integration. The smoothing takes contributions from nearby pixels, which decreases the noise but smooths the resulting image. Increase the smoothing to eliminate streakiness and decrease the smoothing to sharpen the image." />
            <param name="dic_shear_angle" label="Shear angle" type="float" value="0.0" min="0.0" help="The shear angle is the direction of constant value for the shadows and highlights in a DIC image. The gradients in a DIC image run in the direction perpendicular to the shear angle." />
            <param name="dic_decay" label="Decay" type="float" value="0.95" min="0.0" help="The decay setting applies an exponential decay during the process of integration by multiplying the accumulated sum by the decay at each step. This lets the integration recover from accumulated error during the course of the integration, but it also results in diminished intensities in the middle of large objects. Set the decay to a large value, on the order of 1 - 1/diameter of your objects if the intensities decrease toward the middle. Set the decay to a small value if there appears to be a bias in the integration direction." />
        </xml>
    </macros>

    <expand macro="py_requirements"/>
    <expand macro="cmd_modules" />

    <configfiles>

6:bace5a93a97c

<tool id="cp_enhance_or_suppress_features" name="EnhanceOrSuppressFeatures" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>with CellProfiler</description>

    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="feature_speckles">
            <param name="speckles_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size." />
            <param name="speed_accuracy" label="Speed and accuracy" type="select">
                <help>
                    <![CDATA[

            <param name="dic_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" help="Specifies the amount of smoothing of the image in the direction parallel to the shear axis of the image. The line integration method will leave streaks in the image without smoothing as it encounters noisy pixels during the course of the integration. The smoothing takes contributions from nearby pixels, which decreases the noise but smooths the resulting image. Increase the smoothing to eliminate streakiness and decrease the smoothing to sharpen the image." />
            <param name="dic_shear_angle" label="Shear angle" type="float" value="0.0" min="0.0" help="The shear angle is the direction of constant value for the shadows and highlights in a DIC image. The gradients in a DIC image run in the direction perpendicular to the shear angle." />
            <param name="dic_decay" label="Decay" type="float" value="0.95" min="0.0" help="The decay setting applies an exponential decay during the process of integration by multiplying the accumulated sum by the decay at each step. This lets the integration recover from accumulated error during the course of the integration, but it also results in diminished intensities in the middle of large objects. Set the decay to a large value, on the order of 1 - 1/diameter of your objects if the intensities decrease toward the middle. Set the decay to a small value if there appears to be a bias in the integration direction." />
        </xml>
    </macros>

    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">CellProfiler</xref>
        <xref type="biii">cellprofiler</xref>
    </xrefs>

    <expand macro="py_requirements"/>
    <expand macro="cmd_modules" />

    <configfiles>