diff overlay_segmentation_mask.xml @ 0:5f83d67e30f1 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_segmentation_mask.xml	Mon Jan 07 05:38:10 2019 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool name="Overlay Segmentation Mask" id="ip_overlay_segmentation" version="0.0.6">
+   <description>Overlay Segmentation Mask</description>
+   <requirements>
+     <requirement type="package" version="0.14.0">scikit-image</requirement>
+     <requirement type="package" version="3.0.2">matplotlib</requirement>
+     <requirement type="package" version="5.3.0">pillow</requirement>
+     <requirement type="package" version="0.10.0">tifffile</requirement>
+   </requirements>
+   <stdio>
+     <exit_code level="fatal" range="1:"/>
+   </stdio>
+   <command interpreter="python"><![CDATA[overlay_segmentation_mask.py
+       $greyscale 
+       #if str($label_option.label) == '--label'
+         --label --label_color '$label_option.label_color'
+       #end if
+       --thickness $thickness
+       --stroke_color '$stroke_color'
+       '$input_image' '$input_mask' ./tmp.png 
+       && mv ./tmp.png '$output'
+       ]]>
+   </command>
+   <inputs>
+	    <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
+      <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
+      <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
+	    <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
+	    <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
+      <conditional name="label_option">
+        <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
+          <when value=""> </when>
+          <when value="--label">
+      	    <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
+          </when>
+      </conditional>
+   </inputs>
+   <outputs>
+        <data format="png" name="output" />
+   </outputs>
+   <tests>
+   <test> 
+    <conditional name="label_option">
+      <param name="label" value="--label"/>
+      <param name="label_color" value="#ffff00"/>
+    </conditional>
+      <param name="stroke_color" value="#ffaa00"/>
+      <param name="label_option['label']" value="--label"/>
+      <param name="input_image" value="sample.tif"/>
+      <param name="input_mask" value="sample_seg.tif"/>
+      <param name="greyscale" value="--grey"/> 
+      <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
+    </test>
+   </tests>
+   <help>
+This tool overlays a segmentation mask over an image.
+   </help>
+   <citations>
+      <citation type="doi">10.7717/peerj.453</citation>
+   </citations>
+</tool>