Mercurial > repos > thomaswollmann > coordinates_of_roi
diff coordinates_of_roi.xml @ 0:3cbb8ae57f5b draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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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 @@ -0,0 +1,48 @@ +<?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>