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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ commit c045f067a57e8308308cf6329060c7ccd3fc372f |
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modified:
split_labelmap.xml |
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added:
creators.xml tests.xml |
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| diff -r 9db1c22dbe17 -r 7a2e2e3cf836 creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:26:45 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 9db1c22dbe17 -r 7a2e2e3cf836 split_labelmap.xml --- a/split_labelmap.xml Mon Nov 13 22:12:26 2023 +0000 +++ b/split_labelmap.xml Thu Apr 04 15:26:45 2024 +0000 |
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| @@ -1,5 +1,12 @@ <tool id="ip_split_labelmap" name="Split label map using morphological operators" version="0.2-2"> <description></description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + </macros> + <creator> + <expand macro="creators/bmcv"/> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -25,14 +32,16 @@ <tests> <test> <param name="input" value="sample_seg.tif"/> - <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + <expand macro="tests/label_image_diff" name="output" value="out.tif" ftype="tiff"/> </test> </tests> <help> - **What it does** + + **Splits label map using morphological operators.** - Takes a labeled image and outputs a similar file where the labeled parts - of the image that touch (or overlap) are separated by at least 1 pixel (at most 2). + Takes a labeled image and outputs a similar file where the labeled parts + of the image that touch (or overlap) are separated by at least 1 pixel (at most 2 pixels). + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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| diff -r 9db1c22dbe17 -r 7a2e2e3cf836 tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:26:45 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> |