| Previous changeset 1:43c80f3c3b60 (2024-03-13) Next changeset 3:2d1de6e7b113 (2024-04-24) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f |
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modified:
colorize_labels.xml |
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added:
creators.xml tests.xml |
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| diff -r 43c80f3c3b60 -r 3aa2d054848a colorize_labels.xml --- a/colorize_labels.xml Wed Mar 13 19:08:34 2024 +0000 +++ b/colorize_labels.xml Thu Apr 04 15:25:22 2024 +0000 |
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| @@ -1,14 +1,19 @@ <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>with NetworkX</description> <macros> + <import>creators.xml</import> + <import>tests.xml</import> <token name="@TOOL_VERSION@">3.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> + <creator> + <expand macro="creators/bmcv" /> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> <requirements> - <requirement type="package" version="3.2.1">networkx</requirement> + <requirement type="package" version="@TOOL_VERSION@">networkx</requirement> <requirement type="package" version="1.22">numpy</requirement> <requirement type="package" version="0.18.1">scikit-image</requirement> </requirements> @@ -42,18 +47,23 @@ <param name="radius" value="1" /> <param name="bg_label" value="0" /> <param name="bg_color" value="#5a5a5a" /> - <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" /> + <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png"> + <has_image_channels channels="3"/> + </expand> </test> <test> <param name="input" value="input2.tif" /> <param name="radius" value="10" /> <param name="bg_label" value="0" /> <param name="bg_color" value="#ffffff" /> - <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" /> + <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png"> + <has_image_channels channels="3"/> + </expand> </test> </tests> <help> - Colorize a 2-D label map for visualization using greedy coloring. + + **Colorizes a 2-D label map for visualization using greedy coloring.** Label maps are produced by segmentation and other image analysis steps. Direct inspection of label maps can be difficult, @@ -61,6 +71,7 @@ distinguish visually from each other and from the image background. To facilitate the visual inspection of label maps, this tools converts label maps to color images, by assigning each label a unique color. + </help> <citations> <citation type="bibtex"> |
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| diff -r 43c80f3c3b60 -r 3aa2d054848a creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:25:22 2024 +0000 |
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| @@ -0,0 +1,23 @@ +<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/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> |
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| diff -r 43c80f3c3b60 -r 3aa2d054848a tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:25:22 2024 +0000 |
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| @@ -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> |