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comparison points2label.xml @ 2:714a57d6f3a1 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
author imgteam
date Fri, 27 Sep 2024 17:41:06 +0000
parents 3fa3c8e41364
children 2ae122d5d85a
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1:3fa3c8e41364 2:714a57d6f3a1
1 <tool id="ip_points_to_label" name="Points to Label" version="0.3"> 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>Points to Label Image</description> 2 <description></description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.15.4">numpy</requirement> 4 <import>creators.xml</import>
5 <requirement type="package" version="0.14.2">scikit-image</requirement> 5 <import>tests.xml</import>
6 <requirement type="package" version="0.23.4">pandas</requirement> 6 <token name="@TOOL_VERSION@">0.4</token>
7 <requirement type="package" version="0.15.1">tifffile</requirement> 7 <token name="@VERSION_SUFFIX@">0</token>
8 </requirements> 8 </macros>
9 <command detect_errors="aggressive"> 9 <creator>
10 <![CDATA[ 10 <expand macro="creators/bmcv" />
11 python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header 11 </creator>
12 ]]> 12 <edam_operations>
13 </command> 13 <edam_operation>operation_3443</edam_operation>
14 <inputs> 14 </edam_operations>
15 <param name="input" type="data" format="tabular" label="Point CSV file"/> 15 <xrefs>
16 <param name="org_file" type="data" format="tiff" label="Original label image file"/> 16 <xref type="bio.tools">galaxy_image_analysis</xref>
17 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> 17 </xrefs>
18 <requirements>
19 <requirement type="package" version="0.21">scikit-image</requirement>
20 <requirement type="package" version="1.26.4">numpy</requirement>
21 <requirement type="package" version="1.2.4">pandas</requirement>
22 <requirement type="package" version="2024.6.18">tifffile</requirement>
23 <requirement type="package" version="0.3.1">giatools</requirement>
24 </requirements>
25 <command detect_errors="aggressive"><![CDATA[
26
27 python '$__tool_directory__/points2label.py'
28 '$input'
29 '$output'
30 $shapex
31 $shapey
32 $has_header
33 $swap_xy
34 $binary
35
36 ]]></command>
37 <inputs>
38 <param name="input" type="data" format="tabular" label="Tabular list of points"/>
39 <param name="shapex" type="integer" value="500" min="1" label="Width of output image" />
40 <param name="shapey" type="integer" value="500" min="1" label="Height of output image" />
41 <param name="has_header" type="boolean" checked="true" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" help="Turning this off will ignore the first row and assume that the X and Y coordinates correspond to the first and second column, respectively." />
42 <param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" help="Swap the X and Y coordinates, regardless of whether the tabular list has a header or not." />
43 <param name="binary" type="boolean" checked="false" truevalue="--binary True" falsevalue="" optional="true" label="Produce binary image" help="Use the same label for all points (65535)." />
18 </inputs> 44 </inputs>
19 <outputs> 45 <outputs>
20 <data name="output" format="tiff"/> 46 <data name="output" format="tiff" />
21 </outputs> 47 </outputs>
22 <tests> 48 <tests>
49 <!-- Binary / TSV without header -->
23 <test> 50 <test>
24 <param name="input" value="points.tsv"/> 51 <param name="input" value="input1.tsv" />
25 <param name="org_file" value="galaxyIcon_noText.tif"/> 52 <param name="shapex" value="30" />
26 <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/> 53 <param name="shapey" value="20" />
54 <param name="has_header" value="false" />
55 <param name="swap_xy" value="true" />
56 <param name="binary" value="true" />
57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" />
58 </test>
59 <!-- Binary / TSV with header -->
60 <test>
61 <param name="input" value="input2.tsv" />
62 <param name="shapex" value="205" />
63 <param name="shapey" value="84" />
64 <param name="has_header" value="true" />
65 <param name="swap_xy" value="false" />
66 <param name="binary" value="true" />
67 <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tif" ftype="tiff" />
68 </test>
69 <!-- Labeled / TSV with header -->
70 <test>
71 <param name="input" value="input2.tsv" />
72 <param name="shapex" value="205" />
73 <param name="shapey" value="84" />
74 <param name="has_header" value="true" />
75 <param name="swap_xy" value="false" />
76 <param name="binary" value="false" />
77 <expand macro="tests/label_image_diff" name="output" value="output2.tif" ftype="tiff" />
78 </test>
79 <!-- Binary / TSV with header / TSV with labels -->
80 <test>
81 <param name="input" value="input3.tsv" />
82 <param name="shapex" value="200" />
83 <param name="shapey" value="100" />
84 <param name="has_header" value="true" />
85 <param name="swap_xy" value="false" />
86 <param name="binary" value="true" />
87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tif" ftype="tiff" />
88 </test>
89 <!-- Labeled / TSV with header / TSV with labels -->
90 <test>
91 <param name="input" value="input3.tsv" />
92 <param name="shapex" value="200" />
93 <param name="shapey" value="100" />
94 <param name="has_header" value="true" />
95 <param name="swap_xy" value="false" />
96 <param name="binary" value="false" />
97 <expand macro="tests/label_image_diff" name="output" value="output3.tif" ftype="tiff" />
27 </test> 98 </test>
28 </tests> 99 </tests>
29 <help> 100 <help>
30 **What it does**
31 101
32 This tool converts points to a label image. 102 **Converts a tabular list of points to a label map by rasterizing the point coordinates.**
103
104 The created image is a single-channel image with 16 bits per pixel (unsigned integer). The points are
105 rasterized with unique labels, or the value 65535 (white) for binary image output. Pixels not corresponding to
106 any points in the tabular file are assigned the value 0 (black).
107
108 The tabular list of points can either be header-less. In this case, the first and second columns are expected
109 to be the X and Y coordinates, respectively. Otherwise, if a header is present, it is searched for the
110 following column names:
111
112 - ``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.
114 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
115 corresponding radii.
116 - 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.
118
33 </help> 119 </help>
34 <citations> 120 <citations>
35 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 121 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
36 </citations> 122 </citations>
37 </tool> 123 </tool>