comparison imagej2_bunwarpj_elastic_transform.xml @ 1:39b2bc251b2f draft

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

0:301f24849032

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.0">
    <description>with bUnwarpJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_bunwarpj_elastic_transform.py
    --target_image "$target_image"
    --target_image_format $target_image.ext
    --source_image "$source_image"
    --source_image_format $source_image.ext
    --elastic_transformation $elastic_transformation
    --source_out "$source_out"
    --source_out_datatype $source_out_datatype
    --jython_script $__tool_directory__/imagej2_bunwarpj_elastic_transform_jython_script.py
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
        <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
        <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/>
        <param name="source_out_datatype" type="select" label="Save registered source image as format">
            <expand macro="image_datatypes" />
        </param>
    </inputs>
    <outputs>
        <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
            <actions>
                <action type="format">
                    <option type="from_param" name="source_out_datatype" />
                </action>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="target_image" value="dotblot.jpg" />
            <param name="source_image" value="blobs.gif" />
            <param name="elastic_transformation" value="blobs_direct_transf.txt" />
            <param name="source_out_datatype" value="png" />
            <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size" />
        </test>
    </tests>
    <help>
**What it does**

tool.

]]>

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

1:39b2bc251b2f

<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.1">
    <description>with bUnwarpJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <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'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
fi
]]></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="sim_size"/>
        </test>
    </tests>
    <help>
**What it does**

tool.

]]>

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