annotate imagej2_bunwarpj_compare_elastic.xml @ 2:42ba21dc9ea6 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<tool id="imagej2_bunwarpj_compare_elastic" name="Compare opposite elastic deformations" version="@WRAPPER_VERSION@.1">
    <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' '$target_with_ext' &&
bunwarpj -compare_elastic
'$target_with_ext'
'$source_with_ext'
'$target_transformation'
'$source_transformation'
&>'$output_log';
if [[ $? -ne 0 ]]; then
    cat '$output_log' >&2;
else
    grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
fi
]]>
    </command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_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"/>
    </outputs>
    <tests>
        <test>
            <expand macro="test_target_source_images"/>
            <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>