Mercurial > repos > imgteam > morphological_operations
diff morphological_operations.xml @ 1:ad795d260ba8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c045f067a57e8308308cf6329060c7ccd3fc372f
author | imgteam |
---|---|
date | Thu, 04 Apr 2024 15:25:44 +0000 |
parents | f10112b317a1 |
children | 4e25befab102 |
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--- a/morphological_operations.xml Fri Mar 08 11:00:41 2024 +0000 +++ b/morphological_operations.xml Thu Apr 04 15:25:44 2024 +0000 @@ -1,9 +1,14 @@ <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>with SciPy</description> <macros> + <import>creators.xml</import> + <import>tests.xml</import> <token name="@TOOL_VERSION@">1.12.0</token> <token name="@VERSION_SUFFIX@">0</token> </macros> + <creator> + <expand macro="creators/bmcv"/> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -11,7 +16,7 @@ <xref type="biii">scipy</xref> </xrefs> <requirements> - <requirement type="package" version="1.12.0">scipy</requirement> + <requirement type="package" version="@TOOL_VERSION@">scipy</requirement> <requirement type="package" version="0.22.0">scikit-image</requirement> </requirements> <command><![CDATA[ @@ -54,28 +59,28 @@ <param name="operation" value="erosion" /> <param name="selem_shape" value="disk" /> <param name="selem_size" value="1" /> - <output name="result" value="output1_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/binary_image_diff" name="result" value="output1_erosion.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input1.tiff" /> <param name="operation" value="dilation" /> <param name="selem_shape" value="disk" /> <param name="selem_size" value="2" /> - <output name="result" value="output1_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/binary_image_diff" name="result" value="output1_dilation.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input1.tiff" /> <param name="operation" value="opening" /> <param name="selem_shape" value="square" /> <param name="selem_size" value="1" /> - <output name="result" value="output1_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/binary_image_diff" name="result" value="output1_opening.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input1.tiff" /> <param name="operation" value="closing" /> <param name="selem_shape" value="square" /> <param name="selem_size" value="2" /> - <output name="result" value="output1_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/binary_image_diff" name="result" value="output1_closing.tiff" ftype="tiff"/> </test> <!-- Test intensity-based operations (more than two distinct values) --> <test> @@ -83,28 +88,28 @@ <param name="operation" value="erosion" /> <param name="selem_shape" value="disk" /> <param name="selem_size" value="1" /> - <output name="result" value="output3_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/intensity_image_diff" name="result" value="output3_erosion.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input3.png" /> <param name="operation" value="dilation" /> <param name="selem_shape" value="disk" /> <param name="selem_size" value="2" /> - <output name="result" value="output3_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/intensity_image_diff" name="result" value="output3_dilation.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input3.png" /> <param name="operation" value="opening" /> <param name="selem_shape" value="square" /> <param name="selem_size" value="1" /> - <output name="result" value="output3_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/intensity_image_diff" name="result" value="output3_opening.tiff" ftype="tiff"/> </test> <test> <param name="image" value="input3.png" /> <param name="operation" value="closing" /> <param name="selem_shape" value="square" /> <param name="selem_size" value="2" /> - <output name="result" value="output3_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/intensity_image_diff" name="result" value="output3_closing.tiff" ftype="tiff"/> </test> <!-- Test multi-channel image (with two distinct values per channel) --> <test> @@ -112,11 +117,13 @@ <param name="operation" value="fill_holes" /> <param name="selem_shape" value="disk" /> <param name="selem_size" value="1" /> - <output name="result" value="output2_fill_holes.tiff" ftype="tiff" compare="sim_size" delta="10" /> + <expand macro="tests/intensity_image_diff" name="result" value="output2_fill_holes.tiff" ftype="tiff"/> </test> </tests> <help> - Applies a morphological operation to a 2-D image. + + **Applies a morphological operation to a 2-D image.** + For multi-channel images, the operation is applied to each channel separately. The following operations are supported: @@ -126,8 +133,9 @@ - **Opening:** Erosion followed by Dilation. Erases tiny bright spots. - **Closing:** Dilation followed by Erosion. Erases tiny dark holes. - **Fill holes:** Fills the holes (dark areas) in binary images. + </help> <citations> <citation type="doi">10.1038/s41592-019-0686-2</citation> </citations> -</tool> \ No newline at end of file +</tool>