comparison imagej2_analyze_skeleton.xml @ 3:50f2b961b192 draft default tip

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

2:bdee06a1bcfa

<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.1">
    <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' '$input_with_ext' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
'$error_log'
'$input_with_ext'
'$black_background'
'$prune_cycle_method'
'$prune_ends'
'$calculate_largest_shortest_path'
'no'
'$output'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
        <param name="prune_cycle_method" type="select" label="Prune cycle method">

3:50f2b961b192

<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" 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' '$input_with_ext' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
'$input_with_ext'
'$black_background'
'$prune_cycle_method'
'$prune_ends'
'$calculate_largest_shortest_path'
'no'
'$output'
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
        <param name="prune_cycle_method" type="select" label="Prune cycle method">