comparison imagej2_find_maxima.xml @ 3:4409f9eb9433 draft default tip

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

2:6a07f71806bb

<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>

        <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'

    '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">

    </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

3:4409f9eb9433

<tool id="imagej2_find_maxima" name="Find maxima" 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' '$input_with_ext' &&
#if str($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
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_find_maxima_jython_script.py'
'$input_with_ext'
'$scale_when_converting'
'$weighted_rgb_conversions'
$noise_tolerance
'$output_type'

    'tabular'
#else:
    '$output_filename'
    '$input.ext'
#end if
#if $list_or_count
    && mv '$results' '$output';
#else
    && mv '$output_filename' '$output';
#end if
]]></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">

    </inputs>
    <outputs>
        <data name="output" format_source="input">
            <filter>output_type != "List" and output_type != "Count"</filter>
        </data>
        <!-- see comment at output_type parameter
        <data name="results" format="tabular">
            <filter>output_type == "List" or output_type == "Count"</filter>
        </data> -->
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_single_points.gif" compare="image_diff"/>
        </test>
        <test expect_num_outputs="1">
            <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="image_diff"/>
        </test>
        <test expect_num_outputs="1">
            <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="image_diff"/>
        </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