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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
author goeckslab
date Wed, 05 Jun 2024 18:01:54 +0000
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1 <tool id="backsub" name="Background subtraction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2
3 <description>for sequential immunofluorescence images</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10 <expand macro="version_cmd"/>
11
12 <command detect_errors="aggressive"><![CDATA[
13
14 python /background_subtraction/background_sub.py
15
16 ##Supply image
17 --root '$root'
18
19 ##Supply markers
20 --markers '$markers'
21
22 ##Name output image file
23 --output out.ome.tiff
24
25 ##Name output markers file
26 --marker-output out.csv
27
28 ##Additional arguments
29 #if $adv.pixel_size
30 --pixel-size $adv.pixel_size
31 #end if
32
33 #if $adv.tile_size
34 --tile-size $adv.tile_size
35 #end if
36
37 ]]></command>
38
39 <inputs>
40 <param name="root" type="data" format="ome.tiff" optional="false" label="Image to process"/>
41 <param name="markers" type="data" format="csv" optional="false" label="Markers file mapping channels to subtract" help="Expected columns: marker_name, background, exposure, remove"/>
42 <section name="adv" title="Advanced Options" expanded="false">
43 <param name="pixel_size" type="float" optional="true" min=".01" max="1.0" label="Pixel size in microns" help="If not supplied, finds resolution in XML metadata, otherwise defaults to 1"/>
44 <param name="tile_size" type="integer" optional="true" min="256" max="2048" label="Tile size for pyramid generation (default 1024)"/>
45 </section>
46 </inputs>
47
48 <outputs>
49 <data format="ome.tiff" name="image_output" from_work_dir="out.ome.tiff" label="${tool.name} on ${on_string}: Subtracted Image"/>
50 <data format="csv" name="marker_output" from_work_dir="out.csv" label="${tool.name} on ${on_string}: Markers"/>
51 </outputs>
52
53 <tests>
54 <test expect_num_outputs="2">
55 <param name="root" value="test.ome.tiff" />
56 <param name="markers" value="test_markers.csv" />
57 <param name="tile_size" value="256" />
58 <output name="image_output" ftype="ome.tiff">
59 <assert_contents>
60 <has_size value="520000" delta="10000" />
61 </assert_contents>
62 </output>
63 <output name="marker_output" ftype="csv">
64 <assert_contents>
65 <has_n_columns n="3" sep="," />
66 <has_n_lines n="3" />
67 </assert_contents>
68 </output>
69 </test>
70 </tests>
71 <help><![CDATA[
72 **Background autofluorescence subtraction for cyclic imaging data**
73
74 Performs Pixel-by-pixel channel subtraction scaled by exposure times
75 primarily developed for images produced by the COMET platform and to work within
76 the MCMICRO pipeline. Main usecase is autuofluorescence subtraction for
77 multichannel and multicycle images for visualization of images from tissues with
78 high autofluroescence (FFPE), improved segmentation, and quantification (if the
79 previous two usecases aren't necessary, downstream subtraction of
80 autofluorescent signal is encouraged as the script is memory inefficent).
81
82 The markers file (CSV) gives details about the channels and needs to contain
83 the following columns: "marker_name", "background", "exposure", "remove"
84
85 The "marker_name" column should indicate the marker for the acquired channel and all values should be unique.
86 The "background" column should indicate the marker name of the channel which needs to be subtracted.
87 This value must match the "marker_name" value of the background channel.
88 The "exposure" column should contain the exposure time used for channel acquisition,
89 and the measure unit should be consistent across the column. Exposure time is used for scaling the
90 value of the background to be comparable to the processed channel. The "remove" column should contain
91 logical `TRUE` values for channels which should be exluded in the output image.
92
93 *Visit https://github.com/SchapiroLabor/Background_subtraction/ for the most up-to-date information*
94 ]]></help>
95 <expand macro="citations" />
96 </tool>