Mercurial > repos > imgteam > color_deconvolution

annotate color-deconvolution.xml @ 1:29110ca1b63a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:55:58 -0400
parents 85a9449d1dea
children
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29110ca1b63a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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1 <tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.8">
0
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>Color deconvolution</description>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="4.0.0">pillow</requirement>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 <requirement type="package" version="0.18.1">scikit-learn</requirement>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 <requirement type="package" version="1.12">numpy</requirement>
1
29110ca1b63a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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8 <requirement type="package" version="0.15.1">tifffile</requirement>
0
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 </requirements>
1
29110ca1b63a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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10 <command detect_errors="aggressive">
29110ca1b63a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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11 <![CDATA[
0
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 python '$__tool_directory__/color_deconvolution.py' '$input' '$output' '$convtype'
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 ]]>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 </command>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <inputs>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file with 3 channels"/>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 <param name="convtype" type="select" label="Transformation type">
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 <option value="ica" selected="True">ica</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 <option value="pca">pca</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <option value="nmf">nmf</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <option value="fa">fa</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <option value="xyz2rgb">xyz2rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <option value="rgb_from_rbd">rgb_from_rbd</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <option value="rgb_from_hdx">rgb_from_hdx</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <option value="rgb2hsv">rgb2hsv</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <option value="rgb_from_bro">rgb_from_bro</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <option value="bpx_from_rgb">bpx_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <option value="hed_from_rgb">hed_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <option value="rgbcie2rgb">rgbcie2rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <option value="hdx_from_rgb">hdx_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <option value="xyz2luv">xyz2luv</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <option value="rgb2lab">rgb2lab</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <option value="hpx_from_rgb">hpx_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <option value="rgb_from_fgx">rgb_from_fgx</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <option value="rgb_from_gdx">rgb_from_gdx</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <option value="lab2xyz">lab2xyz</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <option value="rgb_from_hpx">rgb_from_hpx</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <option value="lab2rgb">lab2rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <option value="rgb2rgbcie">rgb2rgbcie</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 <option value="bex_from_rgb">bex_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 <option value="xyz2lab">xyz2lab</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 <option value="rgb_from_bex">rgb_from_bex</option>
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43 <option value="fgx_from_rgb">fgx_from_rgb</option>
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44 <option value="rbd_from_rgb">rbd_from_rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 <option value="rgb2hed">rgb2hed</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 <option value="hed2rgb">hed2rgb</option>
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47 <option value="luv2rgb">luv2rgb</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48 <option value="luv2xyz">luv2xyz</option>
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49 <option value="lch2lab">lch2lab</option>
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50 <option value="rgb2luv">rgb2luv</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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51 <option value="ahx_from_rgb">ahx_from_rgb</option>
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52 <option value="rgb_from_hax">rgb_from_hax</option>
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53 <option value="hax_from_rgb">hax_from_rgb</option>
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54 <option value="rgb_from_bpx">rgb_from_bpx</option>
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55 <option value="rgb2xyz">rgb2xyz</option>
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56 <option value="gdx_from_rgb">gdx_from_rgb</option>
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57 <option value="rgb_from_ahx">rgb_from_ahx</option>
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58 <option value="lab2lch">lab2lch</option>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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59 <option value="rgb_from_hed">rgb_from_hed</option>
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60 <option value="bro_from_rgb">bro_from_rgb</option>
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61 <option value="hsv2rgb">hsv2rgb</option>
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data format="tiff" name="output"/>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="input" value="galaxyIcon_noText.png" />
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70 <param name="convtype" value="rgb2hsv" />
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71 <output name="output" ftype="tiff" />
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72 </test>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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73 </tests>
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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74 <help>
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75 **What it does**
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76
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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77 This tools performs several color deconvolution techniques.</help>
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78 <citations>
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79 <citation type="doi">10.7717/peerj.453</citation>
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80 <citation type="bibtex">@inproceedings{sklearn_api,
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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81 author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
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82 Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
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83 Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
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84 and Jaques Grobler and Robert Layton and Jake VanderPlas and
85a9449d1dea planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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85 Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
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86 title = {{API} design for machine learning software: experiences from the scikit-learn
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87 project},
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88 booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
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89 year = {2013},
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90 pages = {108--122},
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91 }</citation>
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92 </citations>
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93 </tool>