diff s3segmenter.xml @ 0:37acf42a824b draft

"planemo upload for repository https://github.com/ohsu-comp-bio/S3segmenter commit d89a61efd4c465a1e6bf5b99b0f78fb19be5bdea-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/s3segmenter.xml	Fri Mar 12 00:18:40 2021 +0000
@@ -0,0 +1,155 @@
+<tool id="s3segmenter" name="s3segmenter" version="@VERSION@.3" profile="17.09">
+    <description>S3segmenter is a Python-based set of functions that generates single cell (nuclei and cytoplasm) label masks.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+ 
+    <expand macro="requirements"/>
+    @VERSION_CMD@
+
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -s '${imagePath}' ./image.tif;
+
+        #if $contoursClassProbPath
+        ln -s ${contoursClassProbPath} ./ContoursPM.tif;
+        #end if
+
+        #if $nucleiClassProbPath
+        ln -s ${nucleiClassProbPath} ./NucleiPM.tif;
+        #end if
+
+        #if $stackProbPath
+        ln -s ${stackProbPath} ./Probabilities.tif;
+        #end if
+
+
+        @CMD_BEGIN@ 
+        --imagePath ./image.tif
+
+        #if $contoursClassProbPath
+        --contoursClassProbPath ./ContoursPM.tif
+        #end if
+
+        #if $nucleiClassProbPath
+        --nucleiClassProbPath ./NucleiPM.tif
+        #end if
+
+        #if $stackProbPath
+        --stackProbPath ./Probabilities.tif
+        #end if
+
+        --mask $mask
+        --probMapChan $probMapChan
+        --crop $crop
+        --cytoMethod $cytoMethod
+        --nucleiFilter $nucleiFilter
+        --nucleiRegion $nucleiRegion
+        --segmentCytoplasm $segmentCytoplasm
+        --cytoDilation $adv.cytoDilation
+        --logSigma $adv.logSigma
+        --CytoMaskChan $adv.CytoMaskChan
+        ##--TissueMaskChan $adv.TissueMaskChan
+        --detectPuncta $adv.detectPuncta
+        --punctaSigma $adv.punctaSigma
+        --punctaSD $adv.punctaSD
+
+        #if not $saveMask
+        --saveMask
+        #end if
+
+        #if not $saveFig
+        --saveFig
+        #end if
+
+        --outputPath .
+    ]]></command>
+
+
+    <inputs>
+
+        <param name="imagePath" type="data" format="tiff" label="Image File"/>
+        <param name="contoursClassProbPath" type="data" format="tiff" optional="true" label="Contours Class Probabilities"/>
+        <param name="nucleiClassProbPath" type="data" format="tiff" optional="true" label="Nuclei Class Probabilities"/>
+        <param name="stackProbPath" type="data" format="tiff" optional="true" label="Stack Probabilities"/>
+        <param name="mask" type="select" label="Choose mask: TMA, tissue, none.">
+            <option selected="true" value="tissue">tissue</option>
+            <option value="TMA">TMA</option>
+            <option value="none">none</option>
+        </param>
+        <param name="probMapChan" type="integer" value="-1" label="Probability Maps Channel"/>
+        <param name="crop" type="select" label="Crop Strategy">
+            <option selected="true" value="noCrop">No Crop</option>
+            <option value="autoCrop">Automatic Crop</option>
+            <option value="dearray">De-array</option>
+            <option value="plate">Plate</option>
+        </param>
+        <param name="cytoMethod" type="select" label="Cyto Method">
+            <option value="hybrid">Hybrid</option>
+            <option selected="true" value="distanceTransform">Distance Transform</option>
+            <option value="bwdistanceTransform">BW Distance Transform</option>
+            <option value="ring">Ring</option>
+        </param>
+        <param name="nucleiFilter" type="select" label="Nuclei Filter">
+            <option selected="true" value="IntPM">IntPM</option>
+            <option value="LoG">LoG</option>
+            <option value="Int">Int</option>
+            <option value="none">none</option>
+        </param>
+        <param name="nucleiRegion" type="select" label="Nuclei Region">
+            <option value="watershedContourDist">watershedContourDist</option>
+            <option selected="true" value="watershedContourInt">watershedContourInt</option>
+            <option value="watershedBWDist">watershedBWDist</option>
+            <option value="dilation">dilation</option>
+            <option value="localThreshold">localThreshold</option>
+        </param>
+        <param name="segmentCytoplasm" type="select" label="Segment Cytoplasm">
+            <option value="segmentCytoplasm">segmentCytoplasm</option>
+            <option selected="true" value="ignoreCytoplasm">ignoreCytoplasm</option>
+        </param>
+        <param name="saveMask" type="boolean" checked="true" label="Save Mask"/>
+        <param name="saveFig" type="boolean" checked="true" label="Save Figure"/>
+
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="cytoDilation" type="integer" value="5" label="Cyto Dilation"/>
+            <param name="logSigma" type="text" value="3 60" label="logSigma"/>
+            <param name="CytoMaskChan" type="text" value="1" label="Cyto Mask Channel"/>
+            <!-- Bug with S3Segmenter code, expects int not list
+            <param name="TissueMaskChan" type="text" value="-1" label="Tissue Mask Channel"/>
+            -->
+            <param name="detectPuncta" type="text" value="-1" label="Detect Puncta"/>
+            <param name="punctaSigma" type="text" value="1" label="Puncta Sigma"/>
+            <param name="punctaSD" type="text" value="4" label="Puncta SD"/>
+        </section>
+        
+
+    </inputs>
+    <outputs>
+        <data format="tiff" name="cell_mask" from_work_dir="*/cellMask.tif" label="cellMasks">
+            <filter>saveMask is True</filter>
+        </data>
+        <data format="tiff" name="nuclei_mask" from_work_dir="*/nucleiMask.tif" label="nucleiMasks">
+            <filter>saveMask is True</filter>
+        </data>
+        <data format="tiff" name="cell_outlines" from_work_dir="*/cellOutlines.tif" label="cellOutlines">
+            <filter>saveFig is True</filter>
+        </data>
+        <data format="tiff" name="nuclei_outlines" from_work_dir="*/nucleiOutlines.tif" label="nucleiOutlines">
+            <filter>saveFig is True</filter>
+        </data>
+    </outputs>
+    <help><![CDATA[
+Inputs are:
+
+1. an .ome.tif (preferably flat field corrected)
+2. a 3-class probability maps derived from a deep learning model such as UNet. Classes include background, nuclei contours, and nuclei foreground.
+
+The centers of each nuclei are obtained by finding local maxima from the nuclei foreground. These are used for marker-controlled watershed constrained by the nuclei contours.
+
+To segment cytoplasm, the nuclei are in turn used for a marker-controlled watershed segmentation constrained by a cytoplasmic marker such as B-catenin. The channel number of this marker must be specified. A 3-pixel annulus around each nucleus will also be used to segment cytoplasm.
+
+The source repository can be found here: https://github.com/HMS-IDAC/S3segmenter
+OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/S3segmenter
+    ]]></help>
+    <expand macro="citations" />
+</tool>