view color-deconvolution.xml @ 3:3006ce5f7a7d draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 98a304667a4ebb40e0e3daf35b9b1da3de5169cc

<tool id="color_deconvolution" name="Color Deconvolution" version="0.5">
  <description>Color deconvolution</description>
  <requirements>
    <requirement type="package" version="0.12.3" >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>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>