Mercurial > repos > iuc > imagej2_analyze_skeleton

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:27:42 -0400
parents 20555566d6ad
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
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3 <description></description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
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7 <expand macro="fiji_requirements" />
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8 <command>
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9 <![CDATA[
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10 python $__tool_directory__/imagej2_analyze_skeleton.py
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11 --input "$input"
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12 --input_datatype $input.ext
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13 --black_background $black_background
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14 --prune_cycle_method $prune_cycle_method
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15 --prune_ends $prune_ends
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16 --calculate_largest_shortest_path $calculate_largest_shortest_path
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17 ##TODO: seel below--show_detailed_info $show_detailed_info
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18 --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py
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19 --output "$output"
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
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24 <expand macro="black_background_param" />
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25 <param name="prune_cycle_method" type="select" label="Prune cycle method">
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26 <option value="none" selected="True">None</option>
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27 <option value="shortest_branch">Shortest branch</option>
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28 <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
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29 <option value="lowest_intensity_branch">Lowest intensity branch</option>
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30 </param>
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31 <param name="prune_ends" type="select" label="Prune ends">
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32 <option value="no" selected="True">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
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36 <option value="no" selected="True">No</option>
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37 <option value="yes">Yes</option>
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38 </param>
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39 <!-- TODO: Uncomment this option when the tool has been enhanced to use the
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40 future "Display labeled skeletons" option. See http://fiji.sc/AnalyzeSkeleton.
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41 <param name="show_detailed_info" type="select" label="Show detailed info">
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42 <option value="no" selected="True">No</option>
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43 <option value="yes">Yes</option>
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44 </param>
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45 -->
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46 </inputs>
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47 <outputs>
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48 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" value="skeletonized_blobs.gif" />
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53 <param name="input_datatype" value="gif" />
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54 <output name="output" file="basic.tabular" ftype="tabular" />
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55 </test>
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56 <test>
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57 <param name="input" value="skeletonized_clown.jpg" />
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58 <param name="input_datatype" value="jpg" />
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59 <param name="prune_cycle_method" value="shortest_branch" />
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60 <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
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61 </test>
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62 <test>
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63 <param name="input" value="skeletonized_blobs.gif" />
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64 <param name="input_datatype" value="gif" />
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65 <param name="calculate_largest_shortest_path" value="yes" />
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66 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
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67 </test>
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68 <test>
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69 <!-- TODO: Change this test and the following test to set "show_detailed_info"
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70 to "yes" when the tool has been enhanced to use the future "Display labeled skeletons"
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71 option. See http://fiji.sc/AnalyzeSkeleton. -->
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72 <param name="input" value="skeletonized_blobs.gif" />
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73 <param name="input_datatype" value="gif" />
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74 <!-- <param name="show_detailed_info" value="yes" /> -->
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75 <output name="output" file="detailed.tabular" ftype="tabular" />
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76 </test>
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77 <test>
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78 <param name="input" value="skeletonized_clown.jpg" />
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79 <param name="input_datatype" value="jpg" />
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80 <param name="prune_cycle_method" value="shortest_branch" />
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81 <param name="calculate_largest_shortest_path" value="yes" />
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82 <!-- <param name="show_detailed_info" value="yes" /> -->
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83 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
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84 </test>
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85 </tests>
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86 <help>
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87
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88 .. class:: warningmark
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89
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90 The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will
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91 automatically be converted to binary before they are analyzed. This step is performed using the
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92 ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
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93 **Black background:** No, **Pad edges when eroding:** No. If these settings are not appropriate,
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94 first manually convert the image to binary using the **Convert to binary (black and white) with
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95 ImageJ2** tool, which allows you to change them.
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96
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97 .. class:: warningmark
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98
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99 The **Skeletonize images** tool produces skeleton images that can be used as input to this tool.
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100 Images that have not been skeletonized will not result in errors, but the results may or may not
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101 be useful.
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102
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103 **What it does**
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104
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105 <![CDATA[
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106 Tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple
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107 points and branches, and measures their average and maximum length. The voxels are classified into
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108 three different categories depending on their 26 neighbors:
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109
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110 - **End-point** voxels: if they have less than 2 neighbors.
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111 - **Junction** voxels: if they have more than 2 neighbors.
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112 - **Slab** voxels: if they have exactly 2 neighbors.
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113
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114 -----
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115
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116 **Options**
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117
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118 - **Prune cycle method**: prune the possible loops in the skeleton.
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119 - **Prune ends**: prunes any branch that ends in an end-point.
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120 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
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121 ]]>
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122 </help>
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123 <citations>
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124 <citation type="doi">10.1002/jemt.20829</citation>
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125 <citation type="doi">10.1038/nmeth.2102</citation>
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126 </citations>
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127 </tool>