annotate imagej2_find_maxima.xml @ 2:6a07f71806bb draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.2">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <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' '$input_with_ext' &&
#if str($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>
            <!--
            This version of Fiji does not produce the same resultsTable
            as the previous version, so eliminating these options until
            there is time to investigate
            <option value="List">List</option>
            <option value="Count">Count</option>
            -->
        </param>
        <param name="exclude_edge_maxima" type="select" label="Exclude edge maxima?">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="light_background" type="select" label="Light background?">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="scale_when_converting" type="select" label="Scale when converting?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
            <option value="yes" selected="True">Yes</option>
            <option value="no">No</option>
        </param>
        <param name="weighted_rgb_conversions" type="select" label="Weighted RGB conversions?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
            <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
        <test>
            <param name="input" value="blobs.gif" />
            <param name="output_type" value="List" />
            <output name="output" file="blobs_list.tabular" />
        </test>
        <test>
            <param name="input" value="blobs.gif" />
            <param name="output_type" value="Count" />
            <output name="output" file="blobs_count.tabular" />
        </test>
        -->
    </tests>
    <help>

**What it does**

Determines the local maxima in an image and creates a binary (mask-like) image of the same size with the
maxima (or one segmented particle per maximum) marked.  For RGB images, maxima of luminance are selected
with the luminance defined as the weighted or unweighted average of the colors depending on the **Scale
when converting** and **Weighted RGB conversions** settings.

- **Scale when converting** (RGB images only) - If "yes", the tool will scale from min--max to 0--255 when converting from 16-bit or 32-bit to 8-bit or to scale from min--max to 0--65535 when converting from 32-bit to 16-bit.

- **Weighted RGB conversions** (RGB images only) - If "yes", the formula gray = 0.299 × red + 0.587 × green + 0.114 × blue is used to convert RGB images to grayscale.  If "no", the formula gray = (red + green + blue) ⁄ 3 is used.

- **Noise Tolerance** - Maxima are ignored if they do not stand out from the surroundings by more than this value (calibrated units for calibrated images). In other words, a threshold is set at the maximum value minus noise tolerance and the contiguous area around the maximum above the threshold is analyzed. For accepting a maximum, this area must not contain any point with a value higher than the maximum. Only one maximum within this area is accepted.

- **Output Type** can be:

 - **Single Points** - Produces an image with one single point per maximum.

 - **Maxima Within Tolerance** - Produces an image with all points within the "Noise Tolerance" for each maximum.

 - **Segmented Particles** - Assumes that each maximum belongs to a particle and segments the image by a watershed algorithm applied to the values of the image.

 - **List** - Produces the list x, y of maxima in the image.

 - **Count** - Produces the number of maxima in the image.

- **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>