comparison imagej2_find_maxima.xml @ 1:e2622ebb5ce4 draft

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

0:29b39f5b0e69

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_find_maxima.py
    --input "$input"
    --input_datatype $input.ext
    --scale_when_converting $scale_when_converting
    --weighted_rgb_conversions $weighted_rgb_conversions
    --noise_tolerance $noise_tolerance
    --output_type $output_type
    --exclude_edge_maxima $exclude_edge_maxima
    --light_background $light_background
    --jython_script $__tool_directory__/imagej2_find_maxima_jython_script.py
    #if str( $output_type ) == "List" or str( $output_type ) == "Count":
        --output "$results"
        --output_datatype "tabular"
    #else:
        --output "$output"
        --output_datatype $output.ext
    #end if
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
        <param name="noise_tolerance" type="integer" value="10" min="0" label="Noise tolerance" help="Maxima are ignored if they do not stand out from the surroundings by more than this value."/>
        <param name="output_type" type="select" label="Output type">
            <option value="Single_Points" selected="True">Single Points</option>
            <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option>
            <option value="Segmented_Particles">Segmented Particles</option>

            <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}: ${output_type}">
            <filter>output_type != "List" and output_type != "Count"</filter>
        </data>
        <data name="results" format="tabular" label="${tool.name} on ${on_string}: ${output_type}">
            <filter>output_type == "List" or output_type == "Count"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif" />
            <output name="output" file="blobs_single_points.gif" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="noise_tolerance" value="13" />
            <param name="output_type" value="Maxima_Within_Tolerance" />
            <output name="output" file="blobs_tolerance.gif" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="noise_tolerance" value="16" />
            <param name="output_type" value="Segmented_Particles" />
            <param name="exclude_edge_maxima" value="yes" />
            <output name="output" file="blobs_segmented.gif" compare="sim_size" />
        </test>
        <!--
        This version of Fiji does not produce the same resultsTable
        as the previous version, so eliminating these options until
        there is time to investigate

- **Exclude Edge Maxima** - Excludes maxima if the area within the noise tolerance surrounding a maximum touches the edge of the image (edge of the selection does not matter).

- **Light Background** - Select "yes" if the image background is brighter than the objects you want to find.

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

1:e2622ebb5ce4

<tool id="imagej2_find_maxima" name="Find maxima" 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' '$input_with_ext' &&
#if str($output_type) == 'List' or str($output_type) == 'Count':
    #set list_or_count = True
#else:
    #set output_filename = '.'.join(['output', $input.ext])
    touch '$output_filename' &&
    #set list_or_count = False
#end if
touch '$error_log' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_find_maxima_jython_script.py'
'$error_log'
'$input_with_ext'
'$scale_when_converting'
'$weighted_rgb_conversions'
$noise_tolerance
'$output_type'
'$exclude_edge_maxima'
'$light_background'
#if $list_or_count:
    '$results'
    'tabular'
#else:
    '$output_filename'
    '$input.ext'
#end if
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    #if $list_or_count:
        mv '$results' '$output';
    #else:
        mv '$output_filename' '$output';
    #end if
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <param name="noise_tolerance" type="integer" value="10" min="0" label="Noise tolerance" help="Maxima are ignored if they do not stand out from the surroundings by more than this value."/>
        <param name="output_type" type="select" label="Output type">
            <option value="Single_Points" selected="True">Single Points</option>
            <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option>
            <option value="Segmented_Particles">Segmented Particles</option>

            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input">
            <filter>output_type != "List" and output_type != "Count"</filter>
        </data>
        <data name="results" format="tabular">
            <filter>output_type == "List" or output_type == "Count"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_single_points.gif" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="noise_tolerance" value="13"/>
            <param name="output_type" value="Maxima_Within_Tolerance"/>
            <output name="output" file="blobs_tolerance.gif" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="noise_tolerance" value="16"/>
            <param name="output_type" value="Segmented_Particles"/>
            <param name="exclude_edge_maxima" value="yes"/>
            <output name="output" file="blobs_segmented.gif" compare="sim_size"/>
        </test>
        <!--
        This version of Fiji does not produce the same resultsTable
        as the previous version, so eliminating these options until
        there is time to investigate

- **Exclude Edge Maxima** - Excludes maxima if the area within the noise tolerance surrounding a maximum touches the edge of the image (edge of the selection does not matter).

- **Light Background** - Select "yes" if the image background is brighter than the objects you want to find.

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