comparison spot_detection_2d.xml @ 5:e8c9e104e109 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e

4:14f9986800fa

<tool id="ip_spot_detection_2d" name="Perform 2D spot detection" version="0.0.3-2" profile="20.05">
    <description></description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="2.9.0">imageio</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
         python '$__tool_directory__/spot_detection_2d.py'
         '$fn_in'
         '$fn_out'
         '$frame_1st'
         '$frame_end'
         '$filter'
         '$ssig'
         '$thres'
         '$typ_intens'
         '$bndy'
    ]]>
    </command>
    <inputs>
        <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
        <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
        <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
        <param name="filter" type="select" label="Choose a detection filter">
            <option value="Gauss" selected="True">Gaussian</option>
            <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option>
        </param>
        <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" />
        <param name="thres" type="float" value="10.0" min="0" max="100" label="Percentage of the global maximal as the threshold for candidate spots" />
        <param name="typ_intens" type="select" label="How to measure the intensities">
            <option value="smoothed" selected="True">Smoothed</option>
            <option value="robust">Robust</option>
        </param>
        <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" />
    </inputs>
    <outputs>
        <data format="tabular" name="fn_out" />
    </outputs>
    <tests>
        <test>
            <param name="fn_in" value="test_img1.tif"/>
            <param name="frame_1st" value="1"/>
            <param name="frame_end" value="0"/>
            <param name="filter" value="Gauss"/>
            <param name="ssig" value="1"/>
            <param name="thres" value="10"/>
            <param name="typ_intens" value="smoothed"/>
            <param name="bndy" value="10"/>
            <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
        </test>
    </tests>
    <help>
    **What it does**

    This tool detects spots and measures the intensities in a 2D image (sequence).
    </help>
    <citations>
        <citation type="doi">10.1097/j.pain.0000000000002642</citation>
    </citations>
</tool>

5:e8c9e104e109

<tool id="ip_spot_detection_2d" name="Perform 2-D spot detection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <token name="@TOOL_VERSION@">0.1</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">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.2.0">giatools</requirement>
        <requirement type="package" version="1.26.4">numpy</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="0.21">scikit-image</requirement>
        <requirement type="package" version="2024.6.18">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
         python '$__tool_directory__/spot_detection_2d.py'
         '$fn_in'
         '$fn_out'
         '$frame_1st'
         '$frame_end'
         '$filter_type'
         '$min_scale'
         '$max_scale'
         '$abs_threshold'
         '$rel_threshold'
         '$boundary'
    ]]>
    </command>
    <inputs>
        <param name="fn_in" type="data" format="tiff" label="Intensity image or a stack of images" />
        <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
        <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
        <param name="filter_type" type="select" label="Detection filter">
            <option value="LoG" selected="True">Laplacian of Gaussian</option>
            <option value="DoG">Difference of Gaussians</option>
            <option value="DoH">Determinant of Hessian</option>
        </param>
        <param name="min_scale" type="float" value="1.0" min="1.0" label="Minimum scale" />
        <param name="max_scale" type="float" value="2.0" min="1.0" label="Maximum scale" />
        <param name="abs_threshold" type="float" value=".25" min="0" label="Minimum filter response (absolute)" help="Filter responses below this threshold will be ignored. Only filter responses above this thresholding will be considered as blobs. This threshold is ignored if the relative threshold (below) corresponds to a higher response." />
        <param name="rel_threshold" type="float" value="0" min="0" max="1" label="Minimum filter response (relative)" help="Same as the absolute threshold (above), but as a fraction of the overall maximum filter response of an image. This threshold is ignored if it corresponds to a response below the absolute threshold." />
        <param name="boundary" type="integer" value="10" min="0" label="Image boundary" help="Width of image boundaries (in pixel) where spots will be ignored." />
    </inputs>
    <outputs>
        <data format="tabular" name="fn_out" />
    </outputs>
    <tests>
        <!-- Multi-frame input -->
        <test>
            <param name="fn_in" value="input1.tif"/>
            <param name="frame_1st" value="1"/>
            <param name="frame_end" value="0"/>
            <param name="filter_type" value="LoG"/>
            <param name="min_scale" value="1"/>
            <param name="max_scale" value="2"/>
            <param name="abs_threshold" value="0"/>
            <param name="rel_threshold" value="0.1"/>
            <param name="boundary" value="10"/>
            <output name="fn_out" value="output1.tsv" ftype="tabular" />
        </test>
        <!-- Single-frame input -->
        <test>
            <param name="fn_in" value="input2.tif"/>
            <param name="frame_1st" value="1"/>
            <param name="frame_end" value="0"/>
            <param name="filter_type" value="LoG"/>
            <param name="min_scale" value="1"/>
            <param name="max_scale" value="2"/>
            <param name="abs_threshold" value="0.04"/>
            <param name="rel_threshold" value="0"/>
            <param name="boundary" value="10"/>
            <output name="fn_out" value="output2.tsv" ftype="tabular" />
        </test>
    </tests>
    <help>

        **Perform spot detection and measure the image intensities.**

        This tool detects spots (blobs) and measures the image intensities in a single-channel 2-D image (or a stack of such images).

        The tool produces a TSV file containing all detections, with the following columns:

        - ``frame``: The frame of the image stack
        - ``pos_x``: The horizontal coordinate of the detection
        - ``pos_y``: The vertical coordinate of the detection
        - ``scale``: The scale at which the detection was found
        - ``radius``: The radius of the detected spot
        - ``intensity``: The mean intensity of the spot

    </help>
    <citations>
        <citation type="doi">10.1097/j.pain.0000000000002642</citation>
    </citations>
</tool>