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annotate binary2label.xml @ 6:364e235bf378 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
author imgteam
date Sat, 03 Jan 2026 14:14:28 +0000
parents 7f8102bdbfa1
children
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
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1 <tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>with giatools</description>
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3 <macros>
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4 <import>creators.xml</import>
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364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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5 <import>tests.xml</import>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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6 <import>validators.xml</import>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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7 <token name="@TOOL_VERSION@">0.7.3</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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9 <xml name="input">
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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10 <!-- JPEG is not allowed because it is a lossy compression that has no strictly constant labels -->
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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11 <param name="input" type="data" format="tiff,zarr,png" label="Binary image">
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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12 <expand macro="validators/is_binary"/>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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13 <yield/>
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14 </param>
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15 </xml>
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16 </macros>
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17 <creator>
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18 <expand macro="creators/bmcv"/>
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19 <expand macro="creators/kostrykin"/>
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20 </creator>
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21 <edam_operations>
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22 <edam_operation>operation_3443</edam_operation>
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23 </edam_operations>
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24 <xrefs>
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25 <xref type="bio.tools">galaxy_image_analysis</xref>
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26 <xref type="bio.tools">giatools</xref>
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27 </xrefs>
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28 <requirements>
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29 <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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30 <requirement type="package" version="1.16.3">scipy</requirement>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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31 <requirement type="package" version="0.12.2">ome-zarr</requirement>
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32 </requirements>
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33 <required_files>
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34 <include type="literal" path="binary2label.py"/>
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35 </required_files>
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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36 <command detect_errors="aggressive"><![CDATA[
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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38 python '$__tool_directory__/binary2label.py'
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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39
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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40 #if $setup.input.extension == "zarr"
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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41 --input '$setup.input.extra_files_path/$setup.input.metadata.store_root'
364e235bf378 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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42 #else
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43 --input '$setup.input'
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44 #end if
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45
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46 --output 'output.tiff'
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47 --params '$params'
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48 --verbose
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49
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50 ]]></command>
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51 <configfiles>
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52 <configfile name="params"><![CDATA[
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53 {
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54
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55 #if str($setup.method) == "watershed"
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56 "min_distance": $setup.min_distance,
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57 #end if
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58
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59 "method": "$setup.method"
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60
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61 }
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62 ]]></configfile>
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63 </configfiles>
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64 <inputs>
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65 <conditional name="setup">
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66 <param name="method" type="select" label="Mode"
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67 help="Connected component analysis assigns unique labels to objects that are separated by 1 pixel or more. Watershed transform can also separate partially overlapping objects, but is only applicable to 2-D image data.">
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68 <option value="cca" selected="true">Connected component analysis</option>
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69 <option value="watershed">Watershed transform</option>
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70 </param>
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71 <when value="cca">
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72 <expand macro="input"/>
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73 </when>
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74 <when value="watershed">
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75 <expand macro="input">
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76 <expand macro="validators/is_2d"/>
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77 </expand>
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78 <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects"/>
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79 </when>
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80 </conditional>
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81 </inputs>
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82 <outputs>
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83 <data format="tiff" name="output" from_work_dir="output.tiff"/>
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84 </outputs>
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85 <tests>
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86 <!-- Tests for 2-D -->
0
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87 <test>
6
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88 <conditional name="setup">
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89 <param name="method" value="cca"/>
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90 <param name="input" value="input/input11.tiff"/>
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91 </conditional>
6
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92 <expand macro="tests/label_image_diff" name="output" value="output/input11-cca.tiff" ftype="tiff"/>
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93 <assert_stdout>
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94 <has_line line="[input] Input image axes: YX"/>
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95 <has_line line="[input] Input image shape: (265, 329)"/>
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96 <has_line line="[input] Input image dtype: uint16"/>
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97 <has_line line="[output] Output image axes: YX"/>
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98 <has_line line="[output] Output image shape: (265, 329)"/>
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99 <has_line line="[output] Output image dtype: uint16"/>
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100 </assert_stdout>
0
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101 </test>
4
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102 <test>
6
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103 <conditional name="setup">
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104 <param name="method" value="watershed"/>
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105 <param name="input" value="input/input11.tiff"/>
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106 <param name="min_distance" value="10"/>
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107 </conditional>
6
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108 <expand macro="tests/label_image_diff" name="output" value="output/input11-watershed.tiff" ftype="tiff"/>
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109 <assert_stdout>
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110 <has_line line="[input] Input image axes: YX"/>
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111 <has_line line="[input] Input image shape: (265, 329)"/>
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112 <has_line line="[input] Input image dtype: uint16"/>
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113 <has_line line="[output] Output image axes: YX"/>
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114 <has_line line="[output] Output image shape: (265, 329)"/>
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115 <has_line line="[output] Output image dtype: uint16"/>
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116 </assert_stdout>
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117 </test>
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118 <!-- Tests for 3-D -->
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119 <test>
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120 <conditional name="setup">
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121 <param name="method" value="cca"/>
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122 <param name="input" value="input/input9.zarr"/>
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123 </conditional>
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124 <!-- `label_image_diff` currently does not support 3-D images: https://github.com/galaxyproject/galaxy/pull/21455 -->
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125 <expand macro="tests/intensity_image_diff" name="output" value="output/input9-cca.tiff" ftype="tiff"/>
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126 <assert_stdout>
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127 <has_line line="[input] Input image axes: ZYX"/>
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128 <has_line line="[input] Input image shape: (2, 100, 100)"/>
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129 <has_line line="[input] Input image dtype: bool"/>
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130 <has_line line="[input] Input image resolution=(1.0, 1.0), unit='um', z_spacing=1.0"/>
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131 <has_line line="[output] Output image axes: ZYX"/>
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132 <has_line line="[output] Output image shape: (2, 100, 100)"/>
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133 <has_line line="[output] Output image dtype: uint16"/>
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134 <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um', z_spacing=1.0"/>
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135 </assert_stdout>
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136 </test>
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137 <test expect_failure="true">
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138 <conditional name="setup">
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139 <param name="method" value="watershed"/>
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140 <param name="input" value="input/input9.zarr"/>
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141 </conditional>
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142 <assert_stderr>
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143 <!-- Rejected by py-script -->
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144 <has_text text='Method "watershed" is not applicable to 3-D images.'/>
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145 </assert_stderr>
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146 <assert_stdout>
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147 <has_line line="[input] Input image axes: ZYX"/>
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148 <has_line line="[input] Input image shape: (2, 100, 100)"/>
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149 <has_line line="[input] Input image dtype: bool"/>
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150 <has_line line="[input] Input image resolution=(1.0, 1.0), unit='um', z_spacing=1.0"/>
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151 </assert_stdout>
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152 </test>
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153 <test expect_failure="true">
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154 <conditional name="setup">
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155 <param name="method" value="watershed"/>
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156 <param name="input" value="input/input9.tiff"/>
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157 </conditional>
6
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158 <assert_stderr>
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159 <!-- Rejected by validator -->
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160 <has_n_lines n="0"/>
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161 </assert_stderr>
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162 <assert_stdout>
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163 <!-- Rejected by validator -->
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164 <has_n_lines n="0"/>
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165 </assert_stdout>
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166 </test>
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167 <!-- Tests for multi-channel images -->
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168 <test expect_failure="true">
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169 <conditional name="setup">
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170 <param name="method" value="cca"/>
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171 <param name="input" value="input/input10.zarr"/>
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172 </conditional>
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173 <assert_stderr>
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174 <!-- Rejected by py-script -->
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175 <has_text text='Multi-channel images are forbidden to avoid confusion with multi-channel labels (e.g., RGB labels).'/>
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176 </assert_stderr>
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177 <assert_stdout>
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178 <has_line line="[input] Input image axes: CYX"/>
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179 <has_line line="[input] Input image shape: (2, 64, 64)"/>
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180 <has_line line="[input] Input image dtype: uint8"/>
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181 <has_line line="[input] Input image resolution=(1.0, 1.0)"/>
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182 </assert_stdout>
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183 </test>
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184 <test expect_failure="true">
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185 <conditional name="setup">
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186 <param name="method" value="cca"/>
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187 <param name="input" value="input/rgb.png"/>
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188 </conditional>
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189 <assert_stderr>
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190 <!-- Rejected by validator -->
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191 <has_n_lines n="0"/>
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192 </assert_stderr>
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193 <assert_stdout>
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194 <!-- Rejected by validator -->
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195 <has_n_lines n="0"/>
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196 </assert_stdout>
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197 </test>
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198 </tests>
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199 <help>
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200
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201 **Converts a binary image to a label map.**
0
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202
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203 This tool assigns each object a unique label.
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204
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205 Individual objects are determined using connected component analysis, or distance transform and watershed.
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206
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207 </help>
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208 <citations>
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209 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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210 </citations>
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211 </tool>