annotate imagej2_bunwarpj_adapt_transform.xml @ 2:fa64e8aed5a5 draft

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

<tool id="imagej2_bunwarpj_adapt_transform" name="Adapt an elastic transformation" 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' '$target_with_ext' &&
bunwarpj -adapt_transform
'$target_with_ext'
'$source_with_ext'
'$input_elastic_transformation'
'$output'
$image_size_factor
&>'$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="input_elastic_transformation" type="data" label="Target inverse transformation"/>
        <param name="image_size_factor" type="float" value="2.0" label="Image size factor" help="Must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)"/>
    </inputs>
    <outputs>
        <data name="output" format="txt"/>
    </outputs>
    <tests>
        <test>
            <expand macro="test_target_source_images"/>
            <param name="input_elastic_transformation" value="source_elastic_transformation.txt"/>
            <output name="output" file="adapted_transformation.txt" ftype="txt"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Transforms the coefficients of an elastic transformation according to a real image
factor.  This is useful, for example, for very large images, where sub-sampled versions
of the image (e.g., 4 times smaller) can be registered with the resulting transformations
adapted to the smaller image size (image factor = 4) so they can be applied to the high
resolution images.

]]>

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