annotate imagej2_bunwarpj_raw_transform.xml @ 0:95b7592729e2 draft

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

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.0">
    <description>with bUnwarpJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_bunwarpj_raw_transform.py
    --target_image "$target_image"
    --target_image_format $target_image.ext
    --source_image "$source_image"
    --source_image_format $source_image.ext
    --raw_transformation $raw_transformation
    --source_out "$source_out"
    --source_out_datatype $source_out_datatype
    --jython_script $__tool_directory__/imagej2_bunwarpj_raw_transform_jython_script.py
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
        <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
        <param format="txt" name="raw_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in raw format"/>
        <param name="source_out_datatype" type="select" label="Save registered source image as format">
            <expand macro="image_datatypes" />
        </param>
    </inputs>
    <outputs>
        <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
            <actions>
                <action type="format">
                    <option type="from_param" name="source_out_datatype" />
                </action>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="target_image" value="dotblot.jpg" />
            <param name="source_image" value="blobs.gif" />
            <param name="raw_transformation" value="source_raw_transformation.txt" />
            <param name="source_out_datatype" value="png" />
            <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size" />
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Applies a raw transformation to an image, producing another image which is deformed according
to the transformation.  The transformation file must be in the same format as the files created
with the **Convert elastic transformation to raw with bUnwarpJ** tool.

]]>

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