annotate imagej2_bunwarpj_compose_elastic.xml @ 1:423400b3c47f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

<tool id="imagej2_bunwarpj_compose_elastic" name="Compose two elastic transformations" version="@WRAPPER_VERSION@.0">
    <description>into a raw transformation with bUnwarpJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <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' '$target_with_ext' &&
bunwarpj -compose_elastic
'$target_with_ext'
'$source_with_ext'
'$target_elastic_transformation'
'$source_elastic_transformation'
'$output'
&>'$output_log';
if [[ $? -ne 0 ]]; then
    cat '$output_log' >&2;
fi
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <param format="txt" name="target_elastic_transformation" type="data" label="Target inverse transformation"/>
        <param format="txt" name="source_elastic_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_elastic_transformation" value="target_elastic_transformation.txt"/>
            <param name="source_elastic_transformation" value="source_elastic_transformation.txt"/>
            <output name="output" file="raw_transformation.txt" compare="contains"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Composes two elastic transformations into a raw transformation. The input files must be in the elastic
transformation format (i.e., the same format format as the files created with the **Save Transformation**
option in the **Align two images with bUnwarpJ** tool), and the output file will be in **raw** format.
.

]]>

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