diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/color_deconvolution.xml	Tue Oct 29 13:49:19 2024 +0000
@@ -0,0 +1,110 @@
+<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>