comparison imagej2_enhance_contrast.xml @ 3:1f92b1da556b draft default tip

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

2:056e74fbbf6c

<tool id="imagej2_enhance_contrast" name="Enhance contrast" 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'
#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'

    '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?">

    </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**

3:1f92b1da556b

<tool id="imagej2_enhance_contrast" name="Enhance contrast" 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 '$__tool_directory__/imagej2_enhance_contrast_jython_script.py'
'$input_with_ext'
'$equalize_histogram_cond.equalize_histogram'
#if $equalize_histogram_cond.equalize_histogram == 'no':
    $equalize_histogram_cond.saturated_pixels
    '$equalize_histogram_cond.normalize'

    'None'
    'no'
#end if
'$output_filename'
'$input.ext'
&& mv '$output_filename' '$output';
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <conditional name="equalize_histogram_cond">
            <param name="equalize_histogram" type="select" label="Equalize histogram?">

    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="equalize_histogram" value="yes"/>
            <output name="output" file="blobs_equalize.gif" compare="image_diff"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="saturated_pixels" value="6.2"/>
            <output name="output" file="blobs_saturate.gif" compare="image_diff"/>
        </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="image_diff"/>
        </test>
    </tests>
    <help>

**What it does**