annotate color_deconvolution.xml @ 3:be70a57d7174 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit 07aba15c8f753d650fee9cdd455896a77086a615

<tool id="ip_color_deconvolution" name="Perform color decomposition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.8</token>
        <token name="@VERSION_SUFFIX@">2</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="0.24.0">scikit-image</requirement>
        <requirement type="package" version="11.0.0">pillow</requirement>
        <requirement type="package" version="1.5.2">scikit-learn</requirement>
        <requirement type="package" version="2.1.2">numpy</requirement>
        <requirement type="package" version="2024.9.20">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[ 
        python '$__tool_directory__/color_deconvolution.py' '$input' '$output' '$convtype'
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file with 3 channels"/>
        <param name="convtype" type="select" label="Transformation type">
            <option value="ica" selected="True">ica</option>
            <option value="pca">pca</option>
            <option value="nmf">nmf</option>
            <option value="fa">fa</option>
            <option value="xyz2rgb">xyz2rgb</option>
            <option value="rgb_from_rbd">rgb_from_rbd</option>
            <option value="rgb_from_hdx">rgb_from_hdx</option>
            <option value="rgb2hsv">rgb2hsv</option>
            <option value="rgb_from_bro">rgb_from_bro</option>
            <option value="bpx_from_rgb">bpx_from_rgb</option>
            <option value="hed_from_rgb">hed_from_rgb</option>
            <option value="rgbcie2rgb">rgbcie2rgb</option>
            <option value="hdx_from_rgb">hdx_from_rgb</option>
            <option value="xyz2luv">xyz2luv</option>
            <option value="rgb2lab">rgb2lab</option>
            <option value="hpx_from_rgb">hpx_from_rgb</option>
            <option value="rgb_from_fgx">rgb_from_fgx</option>
            <option value="rgb_from_gdx">rgb_from_gdx</option>
            <option value="lab2xyz">lab2xyz</option>
            <option value="rgb_from_hpx">rgb_from_hpx</option>
            <option value="lab2rgb">lab2rgb</option>
            <option value="rgb2rgbcie">rgb2rgbcie</option>
            <option value="bex_from_rgb">bex_from_rgb</option>
            <option value="xyz2lab">xyz2lab</option>
            <option value="rgb_from_bex">rgb_from_bex</option>
            <option value="fgx_from_rgb">fgx_from_rgb</option>
            <option value="rbd_from_rgb">rbd_from_rgb</option>
            <option value="rgb2hed">rgb2hed</option>
            <option value="hed2rgb">hed2rgb</option>
            <option value="luv2rgb">luv2rgb</option>
            <option value="luv2xyz">luv2xyz</option>
            <option value="lch2lab">lch2lab</option>
            <option value="rgb2luv">rgb2luv</option>
            <option value="ahx_from_rgb">ahx_from_rgb</option>
            <option value="rgb_from_hax">rgb_from_hax</option>
            <option value="hax_from_rgb">hax_from_rgb</option>
            <option value="rgb_from_bpx">rgb_from_bpx</option>
            <option value="rgb2xyz">rgb2xyz</option>
            <option value="gdx_from_rgb">gdx_from_rgb</option>
            <option value="rgb_from_ahx">rgb_from_ahx</option>
            <option value="lab2lch">lab2lch</option>
            <option value="rgb_from_hed">rgb_from_hed</option>
            <option value="bro_from_rgb">bro_from_rgb</option>
            <option value="hsv2rgb">hsv2rgb</option>
        </param>
    </inputs>
    <outputs>
        <data format="tiff" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="galaxyIcon_noText.png" />
            <param name="convtype" value="rgb2hsv" />
            <expand macro="tests/intensity_image_diff" name="output" value="galaxyIcon_noText.tiff" ftype="tiff"/>
        </test>
    </tests>
    <help>

        **What it does**

        This tools performs several color deconvolution techniques.

    </help>
    <citations>
      <citation type="doi">10.7717/peerj.453</citation>
      <citation type="bibtex">@inproceedings{sklearn_api,
            author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
                      Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
                      Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
                      and Jaques Grobler and Robert Layton and Jake VanderPlas and
                      Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
            title = {{API} design for machine learning software: experiences from the scikit-learn project},
            booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
            year = {2013},
            pages = {108--122},
        }</citation>
    </citations>
</tool>