Merge pull request #64 from goeckslab/wrap-bg-subtract

Wrap bg subtract

tools/backsub/.shed.yml

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+owner: goeckslab
+name: backsub
+description: "Background autofluorescence subtraction for MCMICRO"
+long_description: |
+  "Pixel-by-pixel channel subtraction scaled by exposure times, primarily developed for images produced by the COMET platform and to work within the MCMICRO pipeline. Main usecase is autuofluorescence subtraction for multichannel and multicycle images for visualization of images from tissues with high autofluroescence (FFPE), improved segmentation, and quantification (if the previous two usecases aren't necessary, downstream subtraction of autofluorescent signal is encouraged as the script is memory inefficent)."
+remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction
+homepage_url: https://github.com/SchapiroLabor/Background_subtraction
+categories: 
+  - "Imaging"

tools/backsub/backsub.xml

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+<tool id="backsub" name="Background subtraction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+
+    <description>for sequential immunofluorescence images</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="version_cmd"/>
+
+    <command detect_errors="aggressive"><![CDATA[
+
+        python /background_subtraction/background_sub.py
+
+        ##Supply image
+        --root '$root'
+
+        ##Supply markers
+        --markers '$markers'
+
+        ##Name output image file
+        --output out.ome.tiff
+
+        ##Name output markers file
+        --marker-output out.csv
+
+        ##Additional arguments
+        #if $adv.pixel_size
+        --pixel-size $adv.pixel_size
+        #end if
+
+        #if $adv.tile_size
+        --tile-size $adv.tile_size
+        #end if
+        
+    ]]></command>
+
+    <inputs>
+        <param name="root" type="data" format="ome.tiff" optional="false" label="Image to process"/>
+        <param name="markers" type="data" format="csv" optional="false" label="Markers file mapping channels to subtract" help="Expected columns: marker_name, background, exposure, remove"/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="pixel_size" type="float" optional="true" min=".01" max="1.0" label="Pixel size in microns" help="If not supplied, finds resolution in XML metadata, otherwise defaults to 1"/>
+            <param name="tile_size" type="integer" optional="true" min="256" max="2048" label="Tile size for pyramid generation (default 1024)"/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data format="ome.tiff" name="image_output" from_work_dir="out.ome.tiff" label="${tool.name} on ${on_string}: Subtracted Image"/>
+        <data format="csv" name="marker_output" from_work_dir="out.csv" label="${tool.name} on ${on_string}: Markers"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="root" value="test.ome.tiff" />
+            <param name="markers" value="test_markers.csv" />
+            <param name="tile_size" value="256" />
+            <output name="image_output" ftype="ome.tiff">
+                <assert_contents>
+                    <has_size value="520000" delta="10000" />
+                </assert_contents>
+            </output>
+            <output name="marker_output" ftype="csv">
+                <assert_contents>
+                    <has_n_columns n="3" sep="," />
+                    <has_n_lines n="3" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Background autofluorescence subtraction for cyclic imaging data**
+
+Performs Pixel-by-pixel channel subtraction scaled by exposure times
+primarily developed for images produced by the COMET platform and to work within
+the MCMICRO pipeline. Main usecase is autuofluorescence subtraction for
+multichannel and multicycle images for visualization of images from tissues with
+high autofluroescence (FFPE), improved segmentation, and quantification (if the
+previous two usecases aren't necessary, downstream subtraction of
+autofluorescent signal is encouraged as the script is memory inefficent).
+
+The markers file (CSV) gives details about the channels and needs to contain 
+the following columns: "marker_name", "background", "exposure", "remove"
+
+The "marker_name" column should indicate the marker for the acquired channel and all values should be unique. 
+The "background" column should indicate the marker name of the channel which needs to be subtracted. 
+This value must match the "marker_name" value of the background channel. 
+The "exposure" column should contain the exposure time used for channel acquisition, 
+and the measure unit should be consistent across the column. Exposure time is used for scaling the 
+value of the background to be comparable to the processed channel. The "remove" column should contain 
+logical `TRUE` values for channels which should be exluded in the output image.
+
+*Visit https://github.com/SchapiroLabor/Background_subtraction/ for the most up-to-date information*
+    ]]></help>
+    <expand macro="citations" />
+</tool>

tools/backsub/macros.xml

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+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">ghcr.io/schapirolabor/background_subtraction:v@TOOL_VERSION@</container>
+        </requirements>
+    </xml>
+
+    <xml name="version_cmd">
+        <version_command>echo @TOOL_VERSION@</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41592-021-01308-y</citation>
+        </citations>
+    </xml>
+
+    <token name="@PROFILE@">21.0</token>
+    <token name="@TOOL_VERSION@">0.4.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+</macros>

tools/backsub/test-data/test_markers.csv

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+marker_name,background,exposure,remove
+CHAN_0,,200,
+CHAN_1,CHAN_0,200,