view color-deconvolution.xml @ 2:8fcbcf6509d8 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 92068c64f9a6c3cf59f756b9efc2d561196c6873

<tool id="color_deconvolution" name="Color Deconvolution" version="0.4">
  <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="1.11">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>