Mercurial > repos > bgruening > doclayoutyolo

annotate doclayoutyolo.xml @ 0:28b4dc80d58b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
author bgruening
date Fri, 13 Jun 2025 14:54:15 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
1 <tool id="doclayoutyolo" name="DocLayout-YOLO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
2 <description>Enhancing document layout analysis</description>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
3 <macros>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
4 <token name="@TOOL_VERSION@">0.0.4.1</token>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
6 <token name="@PROFILE@">24.2</token>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
7 </macros>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
8 <creator>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
9 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
10 <person givenName="Anup" familyName="Kumar" email="kumara@informatik.uni-freiburg.de"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
11 </creator>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
12 <requirements>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
13 <container type="docker">quay.io/galaxy/doclayout-yolo:@TOOL_VERSION@</container>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
14 </requirements>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
15 <required_files>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
16 <include path="segment_text_yolo.py"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
17 </required_files>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
18 <command detect_errors="aggressive"><![CDATA[
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
19 python '$__tool_directory__/segment_text_yolo.py'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
20 --yolo_model '$input_yolo_model'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
21 --input_image '$input_image'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
22 --input_image_ext '$input_image.ext'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
23 --input_confidence '$input_confidence'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
24 --input_image_size '$input_image_size'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
25 --output_image '$output_image'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
26 --output_geojson '$output_segmentation_coordinates'
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
27 ]]>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
28 </command>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
29 <inputs>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
30 <param name="input_yolo_model" type="data" format="zip" label="Yolo model" help="Please upload a Yolo model."/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
31 <param name="input_image" type="data" format="tiff,jpg,png" label="Input image" help="Please provide an input image for the analysis."/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
32 <param name="input_confidence" type="float" label="Confidence" value="0.5" min="0.0" max="1.0" help="Set confidence threshold between 0.0 and 1.0 for drawing bounding boxes. Higher values indicate higher probablity of segmentation."/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
33 <param name="input_image_size" type="integer" label="Image size" value="1024" min="1" max="1500" help="Set input image size for image resize by Doclayout Yolo model. Larger values may provide better accuracy in segmentation but could be slower. Lower values might be faster with lower accuracy."/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
34 </inputs>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
35 <outputs>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
36 <data format_source="input_image" name="output_image" label="Segmented image"></data>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
37 <data format="geojson" name="output_segmentation_coordinates" label="Segmented coordinates"></data>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
38 </outputs>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
39 <tests>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
40 <test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
41 <param name="input_yolo_model" value="input_yolo_model.zip" location="https://huggingface.co/juliozhao/DocLayout-YOLO-DocLayNet-Docsynth300K_pretrained/resolve/main/doclayout_yolo_doclaynet_imgsz1120_docsynth_pretrain.pt?download=true"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
42 <param name="input_image" value="input_image_png.png"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
43 <param name="input_confidence" value="0.5"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
44 <param name="input_image_size" value="1024"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
45 <output name="output_image" ftype="png">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
46 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
47 <has_size size="920950" delta="100" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
48 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
49 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
50 <output name="output_segmentation_coordinates" ftype="geojson">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
51 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
52 <has_text text="Polygon" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
53 <has_text text="Feature" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
54 <has_text text="coordinates" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
55 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
56 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
57 </test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
58 <test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
59 <param name="input_yolo_model" value="input_yolo_model.zip" location="https://huggingface.co/juliozhao/DocLayout-YOLO-DocLayNet-Docsynth300K_pretrained/resolve/main/doclayout_yolo_doclaynet_imgsz1120_docsynth_pretrain.pt?download=true"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
60 <param name="input_image" value="input_image_jpg.jpg" location="https://zenodo.org/records/15649779/files/input_image_jpg.jpg?download=1"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
61 <param name="input_confidence" value="0.5"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
62 <param name="input_image_size" value="1024"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
63 <output name="output_image" ftype="jpg">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
64 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
65 <has_size size="2753175" delta="100" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
66 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
67 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
68 <output name="output_segmentation_coordinates" ftype="geojson">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
69 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
70 <has_text text="Polygon" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
71 <has_text text="Feature" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
72 <has_text text="coordinates" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
73 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
74 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
75 </test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
76 <test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
77 <param name="input_yolo_model" value="input_yolo_model.zip" location="https://huggingface.co/juliozhao/DocLayout-YOLO-DocLayNet-Docsynth300K_pretrained/resolve/main/doclayout_yolo_doclaynet_imgsz1120_docsynth_pretrain.pt?download=true"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
78 <param name="input_image" value="input_image_tiff.tif"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
79 <param name="input_confidence" value="0.5"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
80 <param name="input_image_size" value="1024"/>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
81 <output name="output_image" ftype="tiff">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
82 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
83 <has_size size="510756" delta="100" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
84 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
85 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
86 <output name="output_segmentation_coordinates" ftype="geojson">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
87 <assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
88 <has_text text="Polygon" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
89 <has_text text="Feature" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
90 <has_text text="coordinates" />
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
91 </assert_contents>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
92 </output>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
93 </test>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
94 </tests>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
95 <help>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
96 <![CDATA[
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
97 **What it does**
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
98
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
99 The tool takes a Yolo model trained for annotating bounding boxes around text. It takes a pretrained Yolo model and predicts bounding boxes in the input image where any text is found.
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
100 It is based on document layout analysis: https://github.com/opendatalab/DocLayout-YOLO. The Yolo model can be downloaded from: https://huggingface.co/juliozhao/DocLayout-YOLO-DocLayNet-Docsynth300K_pretrained/tree/main
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
101
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
102
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
103 **Input files**
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
104 - Yolo model (as `.pt` file)
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
105 - Input image containing text
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
106 - Confidence score to be used for drawing bounding boxes
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
107 - Image size to be resized to by Yolo model
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
108
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
109 **Output files**
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
110 - Segmented image
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
111 - Coordinates of bounding boxes as Geojson file
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
112
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
113 ]]>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
114 </help>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
115 <citations>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
116 <citation type="bibtex">
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
117 @ARTICLE{zhao2024doclayoutyoloenhancingdocumentlayout,
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
118 Author = {Zhao, Zhiyuan and et al.},
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
119 title = {{DocLayout-YOLO: Enhancing Document Layout Analysis through Diverse Synthetic Data and Global-to-Local Adaptive Perception}},
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
120 url = {https://github.com/opendatalab/DocLayout-YOLO}
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
121 }
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
122 </citation>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
123 </citations>
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
bgruening
parents:
diff changeset
124 </tool>