comparison imagej2_analyze_skeleton.xml @ 1:3272e0439968 draft

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

0:bb84f130a4e1

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_analyze_skeleton.py
    --input "$input"
    --input_datatype $input.ext
    --black_background $black_background
    --prune_cycle_method $prune_cycle_method
    --prune_ends $prune_ends
    --calculate_largest_shortest_path $calculate_largest_shortest_path
    ##TODO: seel below--show_detailed_info $show_detailed_info
    --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py
    --output "$output"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
        <expand macro="black_background_param" />
        <param name="prune_cycle_method" type="select" label="Prune cycle method">
            <option value="none" selected="True">None</option>
            <option value="shortest_branch">Shortest branch</option>
            <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
            <option value="lowest_intensity_branch">Lowest intensity branch</option>

            <option value="yes">Yes</option>
        </param>
        -->
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <output name="output" file="basic.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg" />
            <param name="input_datatype" value="jpg" />
            <param name="prune_cycle_method" value="shortest_branch" />
            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <param name="calculate_largest_shortest_path" value="yes" />
            <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
        </test>
        <test>
            <!-- TODO: Change this test and the following test to set "show_detailed_info"
            to "yes" when the tool has been enhanced to use the future "Display labeled skeletons"
            option.  See http://fiji.sc/AnalyzeSkeleton.  -->
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <!-- <param name="show_detailed_info" value="yes" /> -->
            <output name="output" file="detailed.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg" />
            <param name="input_datatype" value="jpg" />
            <param name="prune_cycle_method" value="shortest_branch" />
            <param name="calculate_largest_shortest_path" value="yes" />
            <!-- <param name="show_detailed_info" value="yes" /> -->
            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>

.. class:: warningmark

1:3272e0439968

<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
    <description></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'
#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' '$input_with_ext' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
'$error_log'
'$input_with_ext'
'$black_background'
'$prune_cycle_method'
'$prune_ends'
'$calculate_largest_shortest_path'
'no'
'$output'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
        <param name="prune_cycle_method" type="select" label="Prune cycle method">
            <option value="none" selected="True">None</option>
            <option value="shortest_branch">Shortest branch</option>
            <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
            <option value="lowest_intensity_branch">Lowest intensity branch</option>

            <option value="yes">Yes</option>
        </param>
        -->
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="skeletonized_blobs.gif"/>
            <output name="output" file="basic.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg"/>
            <param name="prune_cycle_method" value="shortest_branch"/>
            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="skeletonized_blobs.gif"/>
            <param name="calculate_largest_shortest_path" value="yes"/>
            <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg"/>
            <param name="prune_cycle_method" value="shortest_branch"/>
            <param name="calculate_largest_shortest_path" value="yes"/>
            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>

.. class:: warningmark