<tool id="ip_projective_transformation_points" name="Projective Transformation" license="MIT" version="0.1.1" profile="20.05">
    <description>of ROIs defined by pixel (point) coordinates</description>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.2.1">scipy</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
        <requirement type="package" version="1.15.2">numpy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        python '$__tool_directory__/projective_transformation_points.py'
            '$input'
            '$tmat'
            '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="ROIs (pixel coordinates) to be transformed (TSV file)" />
        <param name="tmat" type= "data" format="tabular" label="Transformation matrix (TSV file)" />
    </inputs>
    <outputs>
       <data format="tabular" name="output" />
    </outputs> 
    <tests>
      <test>
        <param name="input" value="in.tabular" />
        <param name="tmat" value="tmat.tabular" />
        <output name="output" value="out.tabular" ftype="tabular" compare="diff" />
      </test>
    </tests>
    <help>
    **What it does**

    This tool performs a projective transformation of regions of interest (ROIs) defined by pixel (point) coordinates with/without labels.

    About the format of point coordinates (and labels) in the input TSV table: 
    1st column: x-coordinate; 
    2nd column: y-coordinate; 
    (optional) more column(s): point label(s) (numerical or categorical).
    The top row of the table will be regarded as column headers.

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>