diff color-deconvolution.xml @ 0:d7bd56ed3d85 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/color-deconvolution.xml	Tue Feb 07 09:56:10 2017 -0500
@@ -0,0 +1,86 @@
+<tool id="color_deconvolution" name="color-deconvolution" version="0.2">
+  <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>
+  <description>Color deconvolution</description>
+  <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="pca" selected="True">pca</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>