view color-deconvolution.xml @ 0:8aa6e767f737 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

<tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.7">
    <description>Color deconvolution</description>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="4.0.0">pillow</requirement>
        <requirement type="package" version="0.18.1">scikit-learn</requirement>
        <requirement type="package" version="1.12">numpy</requirement>
    </requirements>
    <command>
        <![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" />
            <output name="output" 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>