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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
author imgteam
date Wed, 25 Sep 2024 08:19:30 +0000
parents 14f9986800fa
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4:14f9986800fa 5:e8c9e104e109
1 <tool id="ip_spot_detection_2d" name="Perform 2D spot detection" version="0.0.3-2" profile="20.05"> 1 <tool id="ip_spot_detection_2d" name="Perform 2-D spot detection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description></description> 2 <description></description>
3 <macros>
4 <import>creators.xml</import>
5 <token name="@TOOL_VERSION@">0.1</token>
6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros>
8 <creator>
9 <expand macro="creators/bmcv" />
10 </creator>
3 <edam_operations> 11 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 12 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 13 </edam_operations>
6 <xrefs> 14 <xrefs>
7 <xref type="bio.tools">galaxy_image_analysis</xref> 15 <xref type="bio.tools">galaxy_image_analysis</xref>
8 </xrefs> 16 </xrefs>
9 <requirements> 17 <requirements>
10 <requirement type="package" version="2.9.0">imageio</requirement> 18 <requirement type="package" version="0.2.0">giatools</requirement>
11 <requirement type="package" version="1.20.2">numpy</requirement> 19 <requirement type="package" version="1.26.4">numpy</requirement>
12 <requirement type="package" version="1.2.4">pandas</requirement> 20 <requirement type="package" version="1.2.4">pandas</requirement>
13 <requirement type="package" version="0.18.1">scikit-image</requirement> 21 <requirement type="package" version="0.21">scikit-image</requirement>
22 <requirement type="package" version="2024.6.18">tifffile</requirement>
14 </requirements> 23 </requirements>
15 <command detect_errors="aggressive"> 24 <command detect_errors="aggressive">
16 <![CDATA[ 25 <![CDATA[
17 python '$__tool_directory__/spot_detection_2d.py' 26 python '$__tool_directory__/spot_detection_2d.py'
18 '$fn_in' 27 '$fn_in'
19 '$fn_out' 28 '$fn_out'
20 '$frame_1st' 29 '$frame_1st'
21 '$frame_end' 30 '$frame_end'
22 '$filter' 31 '$filter_type'
23 '$ssig' 32 '$min_scale'
24 '$thres' 33 '$max_scale'
25 '$typ_intens' 34 '$abs_threshold'
26 '$bndy' 35 '$rel_threshold'
36 '$boundary'
27 ]]> 37 ]]>
28 </command> 38 </command>
29 <inputs> 39 <inputs>
30 <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" /> 40 <param name="fn_in" type="data" format="tiff" label="Intensity image or a stack of images" />
31 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" /> 41 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
32 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" /> 42 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
33 <param name="filter" type="select" label="Choose a detection filter"> 43 <param name="filter_type" type="select" label="Detection filter">
34 <option value="Gauss" selected="True">Gaussian</option> 44 <option value="LoG" selected="True">Laplacian of Gaussian</option>
35 <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option> 45 <option value="DoG">Difference of Gaussians</option>
46 <option value="DoH">Determinant of Hessian</option>
36 </param> 47 </param>
37 <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" /> 48 <param name="min_scale" type="float" value="1.0" min="1.0" label="Minimum scale" />
38 <param name="thres" type="float" value="10.0" min="0" max="100" label="Percentage of the global maximal as the threshold for candidate spots" /> 49 <param name="max_scale" type="float" value="2.0" min="1.0" label="Maximum scale" />
39 <param name="typ_intens" type="select" label="How to measure the intensities"> 50 <param name="abs_threshold" type="float" value=".25" min="0" label="Minimum filter response (absolute)" help="Filter responses below this threshold will be ignored. Only filter responses above this thresholding will be considered as blobs. This threshold is ignored if the relative threshold (below) corresponds to a higher response." />
40 <option value="smoothed" selected="True">Smoothed</option> 51 <param name="rel_threshold" type="float" value="0" min="0" max="1" label="Minimum filter response (relative)" help="Same as the absolute threshold (above), but as a fraction of the overall maximum filter response of an image. This threshold is ignored if it corresponds to a response below the absolute threshold." />
41 <option value="robust">Robust</option> 52 <param name="boundary" type="integer" value="10" min="0" label="Image boundary" help="Width of image boundaries (in pixel) where spots will be ignored." />
42 </param>
43 <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" />
44 </inputs> 53 </inputs>
45 <outputs> 54 <outputs>
46 <data format="tabular" name="fn_out" /> 55 <data format="tabular" name="fn_out" />
47 </outputs> 56 </outputs>
48 <tests> 57 <tests>
58 <!-- Multi-frame input -->
49 <test> 59 <test>
50 <param name="fn_in" value="test_img1.tif"/> 60 <param name="fn_in" value="input1.tif"/>
51 <param name="frame_1st" value="1"/> 61 <param name="frame_1st" value="1"/>
52 <param name="frame_end" value="0"/> 62 <param name="frame_end" value="0"/>
53 <param name="filter" value="Gauss"/> 63 <param name="filter_type" value="LoG"/>
54 <param name="ssig" value="1"/> 64 <param name="min_scale" value="1"/>
55 <param name="thres" value="10"/> 65 <param name="max_scale" value="2"/>
56 <param name="typ_intens" value="smoothed"/> 66 <param name="abs_threshold" value="0"/>
57 <param name="bndy" value="10"/> 67 <param name="rel_threshold" value="0.1"/>
58 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" /> 68 <param name="boundary" value="10"/>
69 <output name="fn_out" value="output1.tsv" ftype="tabular" />
70 </test>
71 <!-- Single-frame input -->
72 <test>
73 <param name="fn_in" value="input2.tif"/>
74 <param name="frame_1st" value="1"/>
75 <param name="frame_end" value="0"/>
76 <param name="filter_type" value="LoG"/>
77 <param name="min_scale" value="1"/>
78 <param name="max_scale" value="2"/>
79 <param name="abs_threshold" value="0.04"/>
80 <param name="rel_threshold" value="0"/>
81 <param name="boundary" value="10"/>
82 <output name="fn_out" value="output2.tsv" ftype="tabular" />
59 </test> 83 </test>
60 </tests> 84 </tests>
61 <help> 85 <help>
62 **What it does**
63 86
64 This tool detects spots and measures the intensities in a 2D image (sequence). 87 **Perform spot detection and measure the image intensities.**
88
89 This tool detects spots (blobs) and measures the image intensities in a single-channel 2-D image (or a stack of such images).
90
91 The tool produces a TSV file containing all detections, with the following columns:
92
93 - ``frame``: The frame of the image stack
94 - ``pos_x``: The horizontal coordinate of the detection
95 - ``pos_y``: The vertical coordinate of the detection
96 - ``scale``: The scale at which the detection was found
97 - ``radius``: The radius of the detected spot
98 - ``intensity``: The mean intensity of the spot
99
65 </help> 100 </help>
66 <citations> 101 <citations>
67 <citation type="doi">10.1097/j.pain.0000000000002642</citation> 102 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
68 </citations> 103 </citations>
69 </tool> 104 </tool>