# HG changeset patch
# User goeckslab
# Date 1717610514 0
# Node ID bf9f98a7f9367df152ea94cdbd4a6440fc1b9315

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f

diff -r 000000000000 -r bf9f98a7f936 backsub.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/backsub.xml	Wed Jun 05 18:01:54 2024 +0000
@@ -0,0 +1,96 @@
+<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>
diff -r 000000000000 -r bf9f98a7f936 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jun 05 18:01:54 2024 +0000
@@ -0,0 +1,22 @@
+<?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>
diff -r 000000000000 -r bf9f98a7f936 test-data/test.ome.tiff
Binary file test-data/test.ome.tiff has changed
diff -r 000000000000 -r bf9f98a7f936 test-data/test_markers.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_markers.csv	Wed Jun 05 18:01:54 2024 +0000
@@ -0,0 +1,3 @@
+marker_name,background,exposure,remove
+CHAN_0,,200,
+CHAN_1,CHAN_0,200,