<tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <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 output_log = 'output_log.txt'
#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' '$target_with_ext' &&
bunwarpj -compare_elastic_raw
'$target_with_ext'
'$source_with_ext'
'$target_elastic_transformation'
'$source_raw_transformation'
'$output'
2>&1 | tee '$output_log'
&& grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>
        <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <expand macro="test_target_source_images"/>
            <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
            <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
            <output name="output" file="warping_index_raw.txt" compare="contains"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Calculates the warping index of an elastic transformation and a raw transformation. The elastic
transformation file must be in the same format as the files created with the **Save transformation**
option of the **Align two images with bUnwarpJ** tool, while the raw transformation file must be
in the same format as the file produced by the **Convert elastic transformation to raw with bUnwarpJ**
tool.

]]>

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