<tool id="imagecoordinates_flipaxis" name="Switch axis coordinates" version="0.1"> 
  <description>Switches the axes of an image and flips the y axis.</description>
  <requirements> 
    <requirement type="package" version="0.23.4" >pandas</requirement>
  </requirements>
  <command detect_errors="aggressive"> 
        <![CDATA[
        python "$__tool_directory__/imagecoordinates_flipaxis.py" '$input' '$output' $img_height
        $offset_x $offset_y
        ]]> 
  </command>
  <inputs> 
    <param name="input" type="data" format="tabular" label="File with image coordinates"/> 
    <param name="img_height" type="integer" value="100" label="Height of the corresponding image"/>
    <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 name="output" format="tabular"/>
  </outputs>
  <tests>
    <test>
	    <param name="input" value="table.tsv" />
      <output name="output" value="out.tsv" ftype="tabular" />
      <param name="img_height" value="500"/>
    </test>
    <test>
	    <param name="input" value="table.tsv" />
      <output name="output" value="out_offset.tsv" ftype="tabular" />
      <param name="img_height" value="500"/>
      <param name="offset_x" value="1"/>
      <param name="offset_y" value="2"/>
    </test>
  </tests>
  <help>Makes x the horizontal axis (left to right) and y the vertical axis (bottom to top), 
  like in a coordinate system.</help>
  <citations>
      <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
  </citations>
</tool>