comparison imagej2_analyze_particles_binary.xml @ 1:1dd5396c734a draft

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

0:aeb9bb864b8c

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_analyze_particles_binary" name="Analyze particles" version="@WRAPPER_VERSION@.0">
    <description>of binary image</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_analyze_particles_binary.py
    --input "$input"
    --input_datatype $input.ext
    --black_background $black_background
    --size "$size"
    --circularity_min $circularity_min
    --circularity_max $circularity_max
    --show $show
    --exclude_edges $exclude_edges
    --include_holes $include_holes
    --jython_script $__tool_directory__/imagej2_analyze_particles_binary_jython_script.py
    #if str($show) == 'Nothing':
        --display_results "yes"
        --all_results "yes"
    #else:
        --display_results $display_results_cond.display_results
        --all_results $display_results_cond.all_results
        --output_datatype $output.ext
        --output "$output"
    #end if
    --results "$results"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
        <expand macro="black_background_param" />
        <param name="size" type="text" value="0-Infinity" label="Size (pixel^2)" help="Enter a single value and particles smaller than that value will be ignored."/>
        <param name="circularity_min" type="float" value="0.0" label="Circularity minimum" help="Values from 0.0 to 1.0, but less than maximum">
            <validator type="in_range" min="0" max="1"/>
        </param>
        <param name="circularity_max" type="float" value="1.0" label="Circularity maximum" help="Values from 0.0 to 1.0, but greater than minimum">

            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}">
            <filter>show != "Nothing"</filter>
       </data>
        <data format="tabular" name="results" label="${tool.name} on ${on_string}: Results">
            <filter>show == "Nothing" or display_results_cond['display_results'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs_watershed_binary.gif" />
            <param name="show" value="Nothing" />
            <output name="output" file="analyze_particles_nothing.tabular" />
        </test>
        <test>
            <param name="input" value="blobs_watershed_binary.gif" />
            <param name="show" value="Outlines" />
            <output name="output" file="analyze_particles_outlines.gif" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="blobs_watershed_binary.gif" />
            <param name="show" value="Masks" />
            <param name="exclude_edges" value="yes" />
            <param name="include_holes" value="yes" />
            <output name="output" file="analyze_particles_masks.gif" compare="sim_size" />
        </test>
    </tests>
    <help>
.. class:: warningmark

- **Exclude on Edges** - If Yes, particles touching the edge of the image will be ignored.
- **Include Holes** - If Yes, interior holes will be included (set to No to exclude interior holes and to measure particles enclosed by other particles).
]]>

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

1:1dd5396c734a

<tool id="imagej2_analyze_particles_binary" name="Analyze particles" version="@WRAPPER_VERSION@.0">
    <description>of binary image</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <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' '$input_with_ext' &&
#set output_log = 'output_log.txt'
touch '$output_log' &&
#if str($show) == 'Nothing':
    #set display_results = 'yes'
    #set all_results = 'yes'
    #set output_filename = ''
    #set output_datatype = ''
    #set results_filename = $results
#else:
    #set display_results = $display_results_cond.display_results
    #set all_results = $display_results_cond.all_results
    #set output_filename = '.'.join(['output', $input.ext])
    #set output_datatype = $input.ext
    touch '$output_filename' &&
    #if str($display_results_cond.display_results) == 'yes':
        #set results_filename = $results
    #else:
        #set results_filename = ''
    #end if
#end if
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_analyze_particles_binary_jython_script.py'
'$output_log'
'$input'
'$black_background'
'$size'
$circularity_min
$circularity_max
'$show'
'$display_results'
'$all_results'
'$exclude_edges'
'$include_holes'
'$output_filename'
'$output_datatype'
'$results_filename'
&>'$output_log';
#if str($output_filename) != '':
    if [[ $? -ne 0 ]]; then
        cat '$output_log' >&2;
    else
        mv '$output_filename' '$output';
    fi
#else:
    if [[ $? -ne 0 ]]; then
        cat '$output_log' >&2;
    fi
#end if
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
        <param name="size" type="text" value="0-Infinity" label="Size (pixel^2)" help="Enter a single value and particles smaller than that value will be ignored."/>
        <param name="circularity_min" type="float" value="0.0" label="Circularity minimum" help="Values from 0.0 to 1.0, but less than maximum">
            <validator type="in_range" min="0" max="1"/>
        </param>
        <param name="circularity_max" type="float" value="1.0" label="Circularity maximum" help="Values from 0.0 to 1.0, but greater than minimum">

            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input">
            <filter>show != "Nothing"</filter>
       </data>
        <data format="tabular" name="results" label="${tool.name} (results) on ${on_string}">
            <filter>show == "Nothing" or display_results_cond['display_results'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="show" value="Nothing"/>
            <output name="output" file="analyze_particles_nothing.tabular"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="show" value="Outlines"/>
            <output name="output" file="analyze_particles_outlines.gif" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="show" value="Masks"/>
            <param name="exclude_edges" value="yes"/>
            <param name="include_holes" value="yes"/>
            <output name="output" file="analyze_particles_masks.gif" compare="sim_size"/>
        </test>
    </tests>
    <help>
.. class:: warningmark

- **Exclude on Edges** - If Yes, particles touching the edge of the image will be ignored.
- **Include Holes** - If Yes, interior holes will be included (set to No to exclude interior holes and to measure particles enclosed by other particles).
]]>

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