Mercurial > repos > goeckslab > backsub
comparison backsub.xml @ 0:bf9f98a7f936 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
author | goeckslab |
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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> |