Mercurial > repos > thomaswollmann > coordinates_of_roi

<?xml version="1.0"?>
<tool name="Coordinates of ROI" id="ia_coordinates_of_roi" version="0.0.3">
    <description>Coordinates of ROI</description>
    <requirements>
        <requirement type="package" version="0.14.0">scikit-image</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            python '$__tool_directory__/coordinates_of_roi.py'
            '$im'
            '$pixel_table'
            $offset_x $offset_y
            $white_obj
            --threshold $threshold
        ]]>
    </command>
    <inputs>
	<param name="im" type="data" format="png" label="Source file" />
	<param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false" label="Set to Yes if object is white and background black, otherwise set to No" />
	<param name="threshold" type="float" value="0.5" label="Threshold value" />
	<param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" />
	<param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" />
    </inputs>
    <outputs>
       <data format="tabular" name="pixel_table" />
    </outputs>
    <tests>
        <test>
            <param name="im" value="test.png"/>
            <param name="white_obj" value="true"/>
            <output name="pixel_table" value="table.csv" ftype="tabular"/>
        </test>
        <test>
            <param name="im" value="test.png"/>
            <param name="white_obj" value="true"/>
            <param name="offset_x" value="1"/>
            <param name="offset_y" value="2"/>
            <output name="pixel_table" value="table2.csv" ftype="tabular"/>
        </test>
  </tests>
    <help>
        This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI).
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>
author	thomaswollmann
date	Wed, 16 Jan 2019 15:34:10 -0500
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