# HG changeset patch
# User goeckslab
# Date 1662650250 0
# Node ID 53240d7c1fc5066559d4c30d7816a37570f0fe69

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 5fb6aa9066c68d9972b3cc4be13503a952f952a5

diff -r 000000000000 -r 53240d7c1fc5 Dockerfile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Thu Sep 08 15:17:30 2022 +0000
@@ -0,0 +1,5 @@
+ARG VERSION=0.3.1
+
+FROM vanvalenlab/deepcell-applications:${VERSION}
+
+ENTRYPOINT []
diff -r 000000000000 -r 53240d7c1fc5 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Sep 08 15:17:30 2022 +0000
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">quay.io/goeckslab/mesmer:@TOOL_VERSION@</container>
+        </requirements>
+    </xml>
+
+    <xml name="version_cmd">
+        <version_command>@CMD_BEGIN@ --help</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41587-021-01094-0</citation>
+        </citations>
+    </xml>
+
+    <token name="@TOOL_VERSION@">0.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@CMD_BEGIN@">python /usr/src/app/run_app.py mesmer</token>
+</macros>
diff -r 000000000000 -r 53240d7c1fc5 mesmer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mesmer.xml	Thu Sep 08 15:17:30 2022 +0000
@@ -0,0 +1,80 @@
+<tool id="mesmer" name="Mesmer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+    <description>Mesmer for whole-cell segmentation of multiplexed tissue imaging data</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="version_cmd"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+    ln -s '$nuclear_image' 'input.tif' && 
+    @CMD_BEGIN@ 
+    --output-directory ./
+    --output-name 'mask.tif'
+    --nuclear-image 'input.tif'
+    --nuclear-channel $nuclear_channel
+    --compartment $compartment
+    --image-mpp $image_mpp
+    $squeeze
+
+    #if $membrane_select.membrane_segment == "True":
+        --membrane-image '$membrane_select.membrane_image'
+        --membrane-channel '$membrane_select.membrane_channel'
+    #end if
+    ]]></command>
+
+    <inputs>
+        <param name="nuclear_image" type="data" format="tiff, ome.tiff" label="Image containing the nuclear marker(s)"/>
+        <param name="nuclear_channel" type="integer" value="0" label="The numerical index of the channel(s) from nuclear-image"/>
+        <param name="compartment" type="select"  label="Compartment for segmentation prediction: ">
+            <option selected="true" value="whole-cell">Whole cell</option>
+            <option value="nuclear">Nuclear</option>
+        </param>
+        <param name="image_mpp" type="float" value="0.5" label="Resolution of the image in microns-per-pixel"/>
+        <param name="squeeze" type="boolean" truevalue="--squeeze" falsevalue="" checked="false" label="Whether to np.squeeze the outputs before saving"/>
+        <conditional name="membrane_select">
+            <param name="membrane_segment" type="select" label="Segment with Cell Membrane">
+                <option selected="True" value="False">No</option>
+                <option value="True">Yes</option>
+            </param>
+            <when value="True">
+                <param name="membrane_image" type="data" format="tiff, ome.tiff" label="The path to an image containing the membrane marker(s)"/>
+                <param name="membrane_channel" type="integer" value="0"  label="The numerical index of the channel(s) from membrane-image"/>
+            </when>
+            <when value="False" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="nuclear_image" value="test.tiff" />
+            <param name="compartment" value="nuclear" />
+            <param name="membrane_select.membrane_segment" value="False" />
+            <param name="image_mmp" value="0.65" />
+            <param name="squeeze" value="--squeeze" />
+            <output name="mask" ftype="tiff">
+                <assert_contents>
+                    <has_size value="360000" delta="1000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+------
+Mesmer
+------
+
+**Mesmer** is a DeepCell application that uses a pre-trained model for predicting nuclear and whole cell segmentation from multiplex tissue data.
+
+**Inputs**
+1. a multiple tissue image that includes a nuclear marker and optionally cytoplasm/membrane markers
+        
+**Outputs**
+1. the nuclear or whole cell segmentation mask 
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 53240d7c1fc5 test-data/test.tiff
Binary file test-data/test.tiff has changed