<tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.2">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <xref type="biii">imagej2</xref>
    </xrefs>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set error_log = 'output_log.txt'
touch '$error_log' &&

## ImageJ2 requires file extensions to be valid image data types.
#set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
#set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_with_ext' &&
#set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
#set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_with_ext' &&

bunwarpj -raw_transform
'$target_with_ext'
'$source_with_ext'
'$raw_transformation'
'$source_out'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
fi
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
        <param format="txt" name="raw_transformation" type="data" label="Raw 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">
            <actions>
                <action type="format">
                    <option type="from_param" name="source_out_datatype"/>
                </action>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <expand macro="test_target_source_images"/>
            <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>