diff s3segmenter.xml @ 2:96d0d969ebc9 draft default tip

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/s3segmenter commit 0f4f17235c5961c2fd3d4c30180507f66214c11d

--- a/s3segmenter.xml	Fri Mar 11 23:37:49 2022 +0000
+++ b/s3segmenter.xml	Fri Sep 16 20:05:54 2022 +0000
@@ -1,49 +1,49 @@
-<tool id="s3segmenter" name="s3segmenter" version="@VERSION@.0" profile="17.09">
-    <description>S3segmenter is a Python-based set of functions that generates single cell (nuclei and cytoplasm) label masks.</description>
+<tool id="s3segmenter" name="s3segmenter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>single cell (nuclei and cytoplasm) label masks.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
  
     <expand macro="requirements"/>
-    @VERSION_CMD@
+    <expand macro="version_cmd"/>
 
     <command detect_errors="exit_code"><![CDATA[
 
-        ln -s '${imagePath}' ./image.tif;
+        ln -s '${imagePath}' './image.tif' &&
 
         #if $contoursClassProbPath
-        ln -s ${contoursClassProbPath} ./ContoursPM.tif;
+        ln -s '${contoursClassProbPath}' './ContoursPM.tif' &&
         #end if
 
         #if $nucleiClassProbPath
-        ln -s ${nucleiClassProbPath} ./NucleiPM.tif;
+        ln -s '${nucleiClassProbPath}' './NucleiPM.tif' &&
         #end if
 
         #if $stackProbPath
-        ln -s ${stackProbPath} ./Probabilities.tif;
+        ln -s '${stackProbPath}' './Probabilities.tif' &&
         #end if
 
 
-        @CMD_BEGIN@ 
-        --imagePath ./image.tif
+        @CMD_BEGIN@ \$S3SEG_CMD 
+        --imagePath './image.tif'
 
         #if $contoursClassProbPath
-        --contoursClassProbPath ./ContoursPM.tif
+        --contoursClassProbPath './ContoursPM.tif'
         #end if
 
         #if $nucleiClassProbPath
-        --nucleiClassProbPath ./NucleiPM.tif
+        --nucleiClassProbPath './NucleiPM.tif'
         #end if
 
         #if $stackProbPath
-        --stackProbPath ./Probabilities.tif
+        --stackProbPath './Probabilities.tif'
         #end if
 
         --probMapChan $probMapChan
         --crop $crop_select.crop
         
         #if $crop_select.crop == "dearray"
-          --maskPath $crop_select.maskPath
+          --maskPath '$crop_select.maskPath'
         #end if
 
         --cytoMethod $cytoMethod
@@ -63,16 +63,9 @@
         --detectPuncta $adv.detectPuncta
         --punctaSigma $adv.punctaSigma
         --punctaSD $adv.punctaSD
-
-        #if not $saveMask
-        --saveMask
-        #end if
-
-        #if not $saveFig
-        --saveFig
-        #end if
-
-        --outputPath .
+        $saveMask
+        $saveFig
+        --outputPath '.'
     ]]></command>
 
 
@@ -94,6 +87,9 @@
             <when value="dearray">
                 <param name="maskPath" type="data" format="tiff" label="TMA Mask File"/>
             </when>
+            <when value="noCrop" />
+            <when value="autoCrop" />
+            <when value="plate" />
         </conditional>
 
         <param name="cytoMethod" type="select" label="Cyto Method">
@@ -121,17 +117,24 @@
                 <option value="pixellevel">pixellevel</option>
             </param>
             <when value="pixellevel">
-                <param name="pixelThreshold" type="float" value="-1.0" Label="Pixel Threshold"/>
-                <param name="pixelMaskChan" type="text" value="2" Label="Pixel Mask Channel"/>
+                <param name="pixelThreshold" type="float" value="-1.0" label="Pixel Threshold"/>
+                <param name="pixelMaskChan" type="text" value="2" label="Pixel Mask Channel"/>
             </when>
+             <when value="watershedContourDist"/>
+             <when value="watershedContourInt"/>
+             <when value="watershedBWDist"/>
+             <when value="dilation"/>
+             <when value="localThreshold"/>
+             <when value="localMax"/>
+             <when value="bypass"/>
         </conditional>
 
         <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"/>
+        <param argument="saveMask" type="boolean" checked="true" truevalue="--saveMask" falsevalue="" label="Save Mask"/>
+        <param argument="saveFig" type="boolean" checked="true" truevalue="--saveFig" falsevalue="" label="Save Figure"/>
 
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="cytoDilation" type="integer" value="5" label="Cyto Dilation"/>
@@ -161,7 +164,29 @@
             <filter>saveFig is True</filter>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="imagePath" value="test.ome.tiff" />
+            <param name="stackProbPath" value="stack_probabilities.tiff" />
+            <param name="punctaSD" value="4" />
+            <output name="cell_mask" ftype="tiff">
+                <assert_contents>
+                    <has_size value="6600000" delta="1000000" />
+                </assert_contents>
+            </output>
+            <output name="nuclei_mask" ftype="tiff">
+                <assert_contents>
+                    <has_size value="6600000" delta="1000000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
+-------------------        
+S3segmenter
+-------------------        
+**S3segmenter** is a Python-based set of functions that generates single cell (nuclei and cytoplasm) label masks.
+
 Inputs are:
 
 1. an .ome.tif (preferably flat field corrected)
@@ -172,7 +197,6 @@
 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>