comparison 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

2:55bf135d6b0c

<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.2">
    <description>with ImageJ</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

#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 -->

    </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**

3:f72f8e6787cd

<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>

#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 -->

    </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**