Mercurial > repos > thomaswollmann > coordinates_of_roi

diff coordinates_of_roi.xml @ 0:3cbb8ae57f5b draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:34:10 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coordinates_of_roi.xml	Wed Jan 16 15:34:10 2019 -0500
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+<?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>