comparison imagej2_watershed_binary.xml @ 3:29aca8eebdaa draft default tip

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

2:aeae7e29d525

<tool id="imagej2_watershed_binary" name="Perform segmentation using watershed transformation" version="@WRAPPER_VERSION@.2">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

        <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' &&
#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
ln -s '$input.file_name' '$input_with_ext' &&
#set output_filename = '.'.join(['output', $input.ext])
touch '$output_filename' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
'$error_log'
'$input_with_ext'
'$black_background'
'$output_filename'
'$input.ext'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    mv '$output_filename' '$output';
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
    </inputs>

        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_watershed_binary.gif" compare="sim_size"/>
        </test>
    </tests>
    <help>
.. class:: warningmark

3:29aca8eebdaa

<tool id="imagej2_watershed_binary" name="Perform segmentation using watershed transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

        <xref type="biii">imagej2</xref>
    </xrefs>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
#set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
ln -s '$input.file_name' '$input_with_ext' &&
#set output_filename = '.'.join(['output', $input.ext])
touch '$output_filename' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
'$input_with_ext'
'$black_background'
'$output_filename'
'$input.ext'
&& mv '$output_filename' '$output';
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
    </inputs>

        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_watershed_binary.gif" compare="image_diff"/>
        </test>
        <test>
            <param name="input" value="confocal-series-first-channel_threshold_default.tiff"/>
            <param name="black_background" value="yes"/>
            <output name="output" file="confocal-series-first-channel_default_threshold_watershed.tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
.. class:: warningmark