annotate 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

<?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>