view projective_transformation.xml @ 4:37b079c98c38 draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ded1703bcd6e295b26201505edb58381991b265e"

<tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.2" profile="20.05"> 
    <description>of 2D images</description>
    <requirements>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
        <requirement type="package" version="1.6.2">scipy</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        ln -s '$moving' ./in.${moving.ext} && 
        python '$__tool_directory__/projective_transformation.py'
        '$fixed'
        ./in.${moving.ext}
        '$tmat'
        ./out.${moving.ext}
        && mv ./out.${moving.ext} ./result_image
    ]]>
    </command>
    <inputs>
        <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" />
        <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" />
        <param name="tmat" type="data" format="tabular" label="Transformation matrix" />
    </inputs>
    <outputs>
        <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
    </outputs>
    <tests>
        <test>
            <param name="fixed" value="fixed.png"/>
            <param name="moving" value="moving.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
        <test>
            <param name="fixed" value="fixed_rgb.png"/>
            <param name="moving" value="moving_rgb.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
        <test>
            <param name="fixed" value="multi_f.tif"/>
            <param name="moving" value="multi_m.tif"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" />
      </test>
    </tests>
    <help>

**What it does**

    This tool performs a projective transformation of the moving image so that it fits the fixed image. 
    Multi-channel and RGB images are supported.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>