comparison imagej2_enhance_contrast.xml @ 1:ef3de3e84817 draft

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

0:edfc597fb180

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_enhance_contrast.py
    --input "$input"
    --input_datatype $input.ext
    --equalize_histogram $equalize_histogram_cond.equalize_histogram
    #if $equalize_histogram_cond.equalize_histogram == 'no':
        --saturated_pixels $equalize_histogram_cond.saturated_pixels
        --normalize $equalize_histogram_cond.normalize
    #end if
    --jython_script $__tool_directory__/imagej2_enhance_contrast_jython_script.py
    --output_datatype $output.ext
    --output "$output"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
        <conditional name="equalize_histogram_cond">
            <param name="equalize_histogram" type="select" label="Equalize histogram?">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
                <param name="saturated_pixels" type="float" value="0.3" min="0.0" max="100.0" label="Saturated pixels pct" help="Value is percentage of total number of pixels">
                    <validator type="in_range" min="0" exclude_min="true" max="100" />
                </param>
                <param name="normalize" type="select" label="Normalize?">
                    <option value="no" selected="True">No</option>
                    <option value="yes">Yes</option>
                </param>
            </when>
            <when value="yes"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="equalize_histogram" value="yes" />
            <output name="output" file="blobs_equalize.gif" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="saturated_pixels" value="6.2" />
            <output name="output" file="blobs_saturate.gif" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="saturated_pixels" value="13.0" />
            <param name="normalize" value="yes" />
            <output name="output" file="blobs_normalize.gif" compare="sim_size" />
        </test>
    </tests>
    <help>

**What it does**

- **Normalize** - Recalculates the pixel values of the image so the range is equal to the maximum range for the data type, or 0-1.0 for float images. The maximum range is 0-255 for 8-bit images and 0-65535 for 16-bit images.  Normalization of RGB images is not supported, so selecting "yes" is ignored for this image type.

]]>

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

1:ef3de3e84817

<tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.1">
    <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' &&
#set output_filename = '.'.join(['output', $input.ext])
touch '$output_filename' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_enhance_contrast_jython_script.py'
'$error_log'
'$input_with_ext'
'$equalize_histogram_cond.equalize_histogram'
#if $equalize_histogram_cond.equalize_histogram == 'no':
    $equalize_histogram_cond.saturated_pixels
    '$equalize_histogram_cond.normalize'
#else:
    'None'
    'no'
#end if
'$output_filename'
'$input.ext'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    mv '$output_filename' '$output';
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <conditional name="equalize_histogram_cond">
            <param name="equalize_histogram" type="select" label="Equalize histogram?">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
                <param name="saturated_pixels" type="float" value="0.3" min="0.0" max="100.0" label="Saturated pixels pct" help="Value is percentage of total number of pixels">
                    <validator type="in_range" min="0" exclude_min="true" max="100"/>
                </param>
                <param name="normalize" type="select" label="Normalize?">
                    <option value="no" selected="True">No</option>
                    <option value="yes">Yes</option>
                </param>
            </when>
            <when value="yes"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="equalize_histogram" value="yes"/>
            <output name="output" file="blobs_equalize.gif" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="saturated_pixels" value="6.2"/>
            <output name="output" file="blobs_saturate.gif" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="saturated_pixels" value="13.0"/>
            <param name="normalize" value="yes"/>
            <output name="output" file="blobs_normalize.gif" compare="sim_size"/>
        </test>
    </tests>
    <help>

**What it does**

- **Normalize** - Recalculates the pixel values of the image so the range is equal to the maximum range for the data type, or 0-1.0 for float images. The maximum range is 0-255 for 8-bit images and 0-65535 for 16-bit images.  Normalization of RGB images is not supported, so selecting "yes" is ignored for this image type.

]]>

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