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comparison macros.xml @ 0:e434d9b9cd13 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
author iuc
date Thu, 09 Oct 2025 07:42:36 +0000
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-1:000000000000 0:e434d9b9cd13
1 <macros>
2 <token name="@TOOL_VERSION@">3.6.5</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">25.0</token>
5
6 <xml name="requirements">
7 <requirements>
8 <requirement type="package" version="3.10.18">python</requirement>
9 <requirement type="package" version="@TOOL_VERSION@">biapy</requirement>
10 <requirement type="package" version="4.10.0">opencv</requirement>
11 <requirement type="package" version="3.3.3">openexr</requirement>
12 <requirement type="package" version="0.5.3">safetensors</requirement>
13 </requirements>
14 </xml>
15 <xml name="creators">
16 <creator>
17 <person givenName="Daniel" familyName="Franco" url="https://danifranco.github.io/" identifier="https://orcid.org/0000-0002-1109-110X" />
18 </creator>
19 </xml>
20 <xml name="citations">
21 <citations>
22 <citation type="doi">10.1038/s41592-025-02699-y</citation>
23 <yield/>
24 </citations>
25 </xml>
26
27 <!-- Q9 -->
28 <xml name="train_raw_param">
29 <param name="raw_train" type="data" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the training raw images" help="Select the training images; all must have the same number of channels, and each channel should contain the same type of information (see https://biapy.readthedocs.io/en/latest/get_started/how_it_works.html for details)."/>
30 </xml>
31
32 <xml name="train_raw_param_opt">
33 <param name="raw_train" type="data" optional="true" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the training raw images" help="Select the training images; all must have the same number of channels, and each channel should contain the same type of information (see https://biapy.readthedocs.io/en/latest/get_started/how_it_works.html for details)."/>
34 </xml>
35
36 <!-- Q10 -->
37 <xml name="train_gt_param">
38 <param name="gt_train" type="data" format="tiff,tif,png,jpg,h5,csv,txt" multiple="true" label="Specify the training ground truth (target) images" help="Select the ground truth (target) data for training; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."/>
39 </xml>
40 <xml name="train_gt_param_opt">
41 <param name="gt_train" type="data" optional="true" format="tiff,tif,png,jpg,h5,csv,txt" multiple="true" label="Specify the training ground truth (target) images" help="Select the ground truth (target) data for training; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."/>
42 </xml>
43
44 <!-- Q11 -->
45 <xml name="test_raw_param">
46 <param name="raw_test" type="data" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the test raw images" help="Select the test images; all must have the same number of channels, and each channel should contain the same type of information to avoid confusing the model."/>
47 </xml>
48 <xml name="test_raw_param_opt">
49 <param name="raw_test" type="data" format="tiff,tif,png,jpg,h5" optional="true" multiple="true" label="Specify the test raw images" help="Select the test images; all must have the same number of channels, and each channel should contain the same type of information to avoid confusing the model."/>
50 </xml>
51
52 <!-- Q13: REQUIRED test GT -->
53 <xml name="test_gt_param_required">
54 <param name="gt_test"
55 type="data"
56 format="tiff,tif,png,jpg,h5,csv,txt"
57 multiple="true"
58 label="Specify the test ground truth/target images"
59 help="Select the ground truth (target) data for testing; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."
60 optional="false" />
61 </xml>
62
63 <!-- Q13: OPTIONAL test GT -->
64 <xml name="test_gt_param_optional">
65 <param name="gt_test"
66 type="data"
67 format="tiff,tif,png,jpg,h5,csv,txt"
68 multiple="true"
69 label="Specify the test ground truth/target images (optional)"
70 help="Select the ground truth (target) data for testing; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image). If provided, BiaPy will compute workflow-specific evaluation metrics on the test set. See https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."
71 optional="true" />
72 </xml>
73 </macros>