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comparison segmetrics.xml @ 8:4512751bccca draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:32 +0000
parents b6e88e7bf2fa
children
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7:b6e88e7bf2fa 8:4512751bccca
1 <tool id="ip_segmetrics" name="Compute image segmentation and object detection performance measures" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="ip_segmetrics" name="Compute image segmentation and object detection performance measures" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with SegMetrics</description> 2 <description>with SegMetrics</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
4 <token name="@TOOL_VERSION@">1.4</token> 5 <token name="@TOOL_VERSION@">1.4</token>
5 <token name="@VERSION_SUFFIX@">4</token> 6 <token name="@VERSION_SUFFIX@">5</token>
6 </macros> 7 </macros>
8 <creator>
9 <expand macro="creators/bmcv"/>
10 </creator>
7 <edam_operations> 11 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 12 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 13 </edam_operations>
10 <xrefs> 14 <xrefs>
11 <xref type="bio.tools">segmetrics</xref> 15 <xref type="bio.tools">segmetrics</xref>
48 #end for 52 #end for
49 ]]> 53 ]]>
50 </command> 54 </command>
51 <inputs> 55 <inputs>
52 56
53 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" /> 57 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented image(s)" />
54 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" /> 58 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth image(s)" />
55 59
56 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" /> 60 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />
57 61
58 <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" /> 62 <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" />
59 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" /> 63 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" />
313 </conditional> 317 </conditional>
314 </repeat> 318 </repeat>
315 </test> 319 </test>
316 </tests> 320 </tests>
317 <help> 321 <help>
318 This tool permits the computation of image segmentation and object detection performance measures for 2-D image data. 322
323 **Computates image segmentation and object detection performance measures for 2-D image data.**
319 324
320 You can either use a pair of individual input images (a segmented and a ground truth image), or a pair of ZIP archives which contain the segmented and the correspondiong ground truth images. When using a pair of individual images, remember to turn off the "Unzip" option. When using ZIP archives, turn it on instead and make sure that the directory structure is the same for the segmented and the ground truth images. Correspondences are estbalished based on the file names, which should be *identical* for a pair of corresponding images. 325 You can either use a pair of individual input images (a segmented and a ground truth image), or a pair of ZIP archives which contain the segmented and the correspondiong ground truth images. When using a pair of individual images, remember to turn off the "Unzip" option. When using ZIP archives, turn it on instead and make sure that the directory structure is the same for the segmented and the ground truth images. Correspondences are estbalished based on the file names, which should be *identical* for a pair of corresponding images.
321 326
322 If all objects within your segmented images are *uniquely* labeled, you can turn on the "Segmentation is uniquely labeled" switch to speed up the computations. Leave it off otherwise, or if you are unsure. The same accounts for the "Ground truth is uniquely labeled" switch and your ground turth image data. 327 If all objects within your segmented images are *uniquely* labeled, you can turn on the "Segmentation is uniquely labeled" switch to speed up the computations. Leave it off otherwise, or if you are unsure. The same accounts for the "Ground truth is uniquely labeled" switch and your ground turth image data.
328
323 </help> 329 </help>
324 <citations> 330 <citations>
325 <citation type="doi">10.1093/bioinformatics/btu080</citation> 331 <citation type="doi">10.1093/bioinformatics/btu080</citation>
326 <citation type="doi">10.1109/ISBI.2009.5193098</citation> 332 <citation type="doi">10.1109/ISBI.2009.5193098</citation>
327 <citation type="doi">10.1109/ICIP.2003.1246871</citation> 333 <citation type="doi">10.1109/ICIP.2003.1246871</citation>