annotate imagej2_bunwarpj_elastic_transform.xml @ 3:f72f8e6787cd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with ImageJ</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 -elastic_transform
'$target_with_ext'
'$source_with_ext'
'$elastic_transformation'
'$source_out'
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
        <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic 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="elastic_transformation" value="blobs_direct_transf.txt"/>
            <output name="source_out" file="elastic_trans_registered_source1.png" compare="image_diff"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Applies an elastic transformation to an image, producing another image which is elastically
deformed according to the transformation.  The transformation file must be in the same format
as the files created with the **Save Transformation** option in the **Align two images with bUnwarpJ**
tool.

]]>

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