Mercurial > repos > imgteam > color_deconvolution
changeset 3:be70a57d7174 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit 07aba15c8f753d650fee9cdd455896a77086a615
| author | imgteam |
|---|---|
| date | Tue, 29 Oct 2024 13:49:19 +0000 |
| parents | 612aa1478fe1 |
| children | |
| files | color-deconvolution.xml color_deconvolution.xml creators.xml test-data/galaxyIcon_noText.tiff tests.xml |
| diffstat | 5 files changed, 233 insertions(+), 99 deletions(-) [+] |
line wrap: on
line diff
--- a/color-deconvolution.xml Mon Nov 13 22:10:42 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -<tool id="ip_color_deconvolution" name="Perform color decomposition" version="0.8-2"> - <description></description> - <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="0.14.2">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> - <requirement type="package" version="0.15.1">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" /> - <output name="output" 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>
--- /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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Tue Oct 29 13:49:19 2024 +0000 @@ -0,0 +1,28 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Tue Oct 29 13:49:19 2024 +0000 @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros>