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comparison points2label.xml @ 3:2ae122d5d85a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
author imgteam
date Wed, 23 Apr 2025 14:37:31 +0000
parents 714a57d6f3a1
children 64c155acb864
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2:714a57d6f3a1 3:2ae122d5d85a
1 <tool id="ip_points_to_label" name="Convert point coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="ip_points_to_label" name="Convert point coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>creators.xml</import> 4 <import>creators.xml</import>
5 <import>tests.xml</import> 5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">0.4</token> 6 <token name="@TOOL_VERSION@">0.4.1</token>
7 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros> 8 </macros>
9 <creator> 9 <creator>
10 <expand macro="creators/bmcv" /> 10 <expand macro="creators/bmcv" />
11 </creator> 11 </creator>
44 </inputs> 44 </inputs>
45 <outputs> 45 <outputs>
46 <data name="output" format="tiff" /> 46 <data name="output" format="tiff" />
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
49 <!-- Binary / TSV without header --> 49 <!-- Binary / TSV without header / Points -->
50 <test> 50 <test>
51 <param name="input" value="input1.tsv" /> 51 <param name="input" value="input1.tsv" />
52 <param name="shapex" value="30" /> 52 <param name="shapex" value="30" />
53 <param name="shapey" value="20" /> 53 <param name="shapey" value="20" />
54 <param name="has_header" value="false" /> 54 <param name="has_header" value="false" />
55 <param name="swap_xy" value="true" /> 55 <param name="swap_xy" value="true" />
56 <param name="binary" value="true" /> 56 <param name="binary" value="true" />
57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" /> 57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" />
58 </test> 58 </test>
59 <!-- Binary / TSV with header --> 59 <!-- Binary / TSV with header / Circles -->
60 <test> 60 <test>
61 <param name="input" value="input2.tsv" /> 61 <param name="input" value="input2.tsv" />
62 <param name="shapex" value="205" /> 62 <param name="shapex" value="205" />
63 <param name="shapey" value="84" /> 63 <param name="shapey" value="84" />
64 <param name="has_header" value="true" /> 64 <param name="has_header" value="true" />
65 <param name="swap_xy" value="false" /> 65 <param name="swap_xy" value="false" />
66 <param name="binary" value="true" /> 66 <param name="binary" value="true" />
67 <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tif" ftype="tiff" /> 67 <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tif" ftype="tiff" />
68 </test> 68 </test>
69 <!-- Labeled / TSV with header --> 69 <!-- Labeled / TSV with header / Circles -->
70 <test> 70 <test>
71 <param name="input" value="input2.tsv" /> 71 <param name="input" value="input2.tsv" />
72 <param name="shapex" value="205" /> 72 <param name="shapex" value="205" />
73 <param name="shapey" value="84" /> 73 <param name="shapey" value="84" />
74 <param name="has_header" value="true" /> 74 <param name="has_header" value="true" />
75 <param name="swap_xy" value="false" /> 75 <param name="swap_xy" value="false" />
76 <param name="binary" value="false" /> 76 <param name="binary" value="false" />
77 <expand macro="tests/label_image_diff" name="output" value="output2.tif" ftype="tiff" /> 77 <expand macro="tests/label_image_diff" name="output" value="output2.tif" ftype="tiff" />
78 </test> 78 </test>
79 <!-- Binary / TSV with header / TSV with labels --> 79 <!-- Binary / TSV with header / TSV with labels / Circles -->
80 <test> 80 <test>
81 <param name="input" value="input3.tsv" /> 81 <param name="input" value="input3.tsv" />
82 <param name="shapex" value="200" /> 82 <param name="shapex" value="200" />
83 <param name="shapey" value="100" /> 83 <param name="shapey" value="100" />
84 <param name="has_header" value="true" /> 84 <param name="has_header" value="true" />
85 <param name="swap_xy" value="false" /> 85 <param name="swap_xy" value="false" />
86 <param name="binary" value="true" /> 86 <param name="binary" value="true" />
87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tif" ftype="tiff" /> 87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tif" ftype="tiff" />
88 </test> 88 </test>
89 <!-- Labeled / TSV with header / TSV with labels --> 89 <!-- Labeled / TSV with header / TSV with labels / Circles -->
90 <test> 90 <test>
91 <param name="input" value="input3.tsv" /> 91 <param name="input" value="input3.tsv" />
92 <param name="shapex" value="200" /> 92 <param name="shapex" value="200" />
93 <param name="shapey" value="100" /> 93 <param name="shapey" value="100" />
94 <param name="has_header" value="true" /> 94 <param name="has_header" value="true" />
95 <param name="swap_xy" value="false" /> 95 <param name="swap_xy" value="false" />
96 <param name="binary" value="false" /> 96 <param name="binary" value="false" />
97 <expand macro="tests/label_image_diff" name="output" value="output3.tif" ftype="tiff" /> 97 <expand macro="tests/label_image_diff" name="output" value="output3.tif" ftype="tiff" />
98 </test>
99 <!-- Labeled / TSV with header / TSV with labels / Rectangles -->
100 <test>
101 <param name="input" value="input4.tsv" />
102 <param name="shapex" value="200" />
103 <param name="shapey" value="100" />
104 <param name="has_header" value="true" />
105 <param name="swap_xy" value="false" />
106 <param name="binary" value="false" />
107 <expand macro="tests/label_image_diff" name="output" value="output4.tif" ftype="tiff" />
98 </test> 108 </test>
99 </tests> 109 </tests>
100 <help> 110 <help>
101 111
102 **Converts a tabular list of points to a label map by rasterizing the point coordinates.** 112 **Converts a tabular list of points to a label map by rasterizing the point coordinates.**
111 121
112 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates. 122 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates.
113 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates. 123 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates.
114 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the 124 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
115 corresponding radii. 125 corresponding radii.
126 - If ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present, then the points will be rasterized
127 as rectangles of the corresponding size.
116 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization 128 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
117 (unless "Produce binary image" is activated). Different points are allowed to use the same label. 129 (unless "Produce binary image" is activated). Different points are allowed to use the same label.
118 130
119 </help> 131 </help>
120 <citations> 132 <citations>