comparison imagej2_bunwarpj_compare_elastic.xml @ 0:b95f87118c6f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

0:b95f87118c6f

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_bunwarpj_compare_elastic" name="Compare opposite elastic deformations" version="@WRAPPER_VERSION@.0">
    <description>by warping index with bUnwarpJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_bunwarpj_compare_elastic.py
    --target_image "$target_image"
    --target_image_format $target_image.ext
    --source_image "$source_image"
    --source_image_format $source_image.ext
    --target_transformation "$target_transformation"
    --source_transformation "$source_transformation"
    --output "$output"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
        <param format="txt" name="target_transformation" type="data" label="Target inverse transformation"/>
        <param format="txt" name="source_transformation" type="data" label="Source direct transformation"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}: Warping index" />
    </outputs>
    <tests>
        <test>
            <param name="target_image" value="dotblot.jpg" />
            <param name="source_image" value="blobs.gif" />
            <param name="target_transformation" value="target_elastic_transformation.txt" />
            <param name="source_transformation" value="source_elastic_transformation.txt" />
            <output name="output" file="warping_index.txt" />
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Calculates the warping index of two elastic transformations, i.e. the average of the geometrical distance
between every pixel and its version after applying both transformations (direct and inverse). This value
is given as a result. The transformation files must be in the same format format as the files created with
the **Save Transformation** option in the **Align two images with bUnwarpJ** tool.

]]>

    </help>
    <expand macro="bunwarpj_citations" />
</tool>