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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit df96ae15da34285b0a9d435a48924665fff37d6a
author imgteam
date Sat, 04 Apr 2026 21:22:07 +0000
parents 227e8928af6e
children
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2:227e8928af6e 3:d45a07063da1
2 <description>with NumPy</description> 2 <description>with NumPy</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import> 4 <import>creators.xml</import>
5 <import>tests.xml</import> 5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">2.3.5</token> 6 <token name="@TOOL_VERSION@">2.3.5</token>
7 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">1</token>
8 </macros> 8 </macros>
9 <creator> 9 <creator>
10 <expand macro="creators/bmcv"/> 10 <expand macro="creators/bmcv"/>
11 <expand macro="creators/kostrykin"/> 11 <expand macro="creators/kostrykin"/>
12 </creator> 12 </creator>
16 <xrefs> 16 <xrefs>
17 <xref type="bio.tools">galaxy_image_analysis</xref> 17 <xref type="bio.tools">galaxy_image_analysis</xref>
18 </xrefs> 18 </xrefs>
19 <requirements> 19 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">numpy</requirement> 20 <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
21 <requirement type="package" version="0.5.2">giatools</requirement> 21 <requirement type="package" version="0.7.3">giatools</requirement>
22 <requirement type="package" version="2025.10.16">tifffile</requirement>
23 </requirements> 22 </requirements>
23 <required_files>
24 <include type="glob" path="*.py"/>
25 </required_files>
24 <command detect_errors="aggressive"><![CDATA[ 26 <command detect_errors="aggressive"><![CDATA[
25 27
26 mkdir output && 28 mkdir output &&
27 python '$__tool_directory__/split.py' 29 python '$__tool_directory__/split.py'
28 30
29 '$input' 31 '$input'
30 '$axis' 32 '$axis'
31 output 33 output
32 34
35 $offset
36 $step
33 $squeeze 37 $squeeze
38
39 #if str($count) != ""
40 --count $count
41 #end if
34 42
35 ]]></command> 43 ]]></command>
36 <inputs> 44 <inputs>
37 <param name="input" type="data" format="tiff,png" label="Image to split" /> 45 <param name="input" type="data" format="tiff,png" label="Image to split"/>
38 <param name="axis" type="select" label="Axis to split along"> 46 <param name="axis" type="select" label="Axis to split along">
39 <option value="T">T-axis (split the frames of a temporal image sequence)</option> 47 <option value="T">T-axis (split the frames of a temporal image sequence)</option>
40 <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option> 48 <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option>
41 <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option> 49 <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option>
42 <option value="S">S-axis (split the samples of an image or image sequence)</option> 50 <option value="S">S-axis (split the samples of an image or image sequence)</option>
43 <option value="Q">Q-axis (other or unknown axis)</option> 51 <option value="Q">Q-axis (other or unknown axis)</option>
44 <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</option> 52 <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</option>
45 </param> 53 </param>
46 <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images" 54 <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images"
47 help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained." /> 55 help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained."/>
56 <param name="offset" type="integer" value="0" min="0" label="Offset"
57 help="Number of slices to skip at the beginning."/>
58 <param name="step" type="integer" value="1" min="1" label="Step"
59 help="Number of slices between extracted images (each slice is extracted for a value of 1, each second slice is extracted for a value of two, and so on)."/>
60 <param name="count" type="integer" optional="true" min="1" label="Count"
61 help="Maximum number of slices to extract."/>
48 </inputs> 62 </inputs>
49 <outputs> 63 <outputs>
50 <collection type="list" name="output" label="Split ${on_string} along ${axis} axis"> 64 <collection type="list" name="output" label="Split ${on_string} along ${axis} axis">
51 <discover_datasets directory="output" pattern="__name__" format="tiff" /> 65 <discover_datasets directory="output" pattern="__name__" format="tiff"/>
52 </collection> 66 </collection>
53 </outputs> 67 </outputs>
54 <tests> 68 <tests>
55 69
56 <!-- PNG tests --> 70 <!-- PNG tests -->
64 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/> 78 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/>
65 </output_collection> 79 </output_collection>
66 <assert_stdout> 80 <assert_stdout>
67 <has_line line="Input image axes: YXC"/> 81 <has_line line="Input image axes: YXC"/>
68 <has_line line="Input image shape: (32, 32, 3)"/> 82 <has_line line="Input image shape: (32, 32, 3)"/>
69 <has_line line="Writing 3 image(s)"/> 83 <has_line line="Writing 3 out of 3 image(s)"/>
70 <has_line line="Output axes: YXC"/> 84 <has_line line="Output axes: YXC"/>
71 <has_line line="Output shape: (32, 32, 1)"/> 85 <has_line line="Output shape: (32, 32, 1)"/>
72 </assert_stdout> 86 </assert_stdout>
73 </test> 87 </test>
74 <test> 88 <test>
77 <param name="squeeze" value="false" /> 91 <param name="squeeze" value="false" />
78 <output_collection name="output" type="list" count="1"> 92 <output_collection name="output" type="list" count="1">
79 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/> 93 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/>
80 </output_collection> 94 </output_collection>
81 <assert_stdout> 95 <assert_stdout>
82 <has_line line="Not a TIFF file"/> 96 <has_line line="Found 1 image(s) in file"/>
83 <has_line line="Writing 1 image(s)"/> 97 <has_line line="Writing 1 out of 1 image(s)"/>
84 <has_line line="Output axes: YXC"/> 98 <has_line line="Output axes: YXC"/>
85 <has_line line="Output shape: (32, 32, 3)"/> 99 <has_line line="Output shape: (32, 32, 3)"/>
86 </assert_stdout> 100 </assert_stdout>
87 </test> 101 </test>
88 102
89 <!-- TIFF tests --> 103 <!-- TIFF tests -->
90 <test> 104 <test>
91 <param name="input" value="zcyx.tiff" /> 105 <param name="input" value="zcyx.tiff"/>
92 <param name="axis" value="Z" /> 106 <param name="axis" value="Z"/>
93 <param name="squeeze" value="false" /> 107 <param name="squeeze" value="false"/>
94 <output_collection name="output" type="list" count="25"> 108 <param name="offset" value="9"/>
95 <expand macro="tests/intensity_image_diff/element" name="01.tiff" value="zcyx_slice01.tiff" ftype="tiff"/> 109 <param name="step" value="2"/>
96 <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/> 110 <param name="count" value="5"/>
111 <output_collection name="output" type="list" count="5">
112 <expand macro="tests/intensity_image_diff/element" name="10.tiff" value="zcyx_slice10.tiff" ftype="tiff"/>
113 <expand macro="tests/intensity_image_diff/element" name="18.tiff" value="zcyx_slice18.tiff" ftype="tiff"/>
97 </output_collection> 114 </output_collection>
98 <assert_stdout> 115 <assert_stdout>
99 <has_line line="Input image axes: ZCYX"/> 116 <has_line line="Input image axes: ZCYX"/>
100 <has_line line="Input image shape: (25, 2, 50, 50)"/> 117 <has_line line="Input image shape: (25, 2, 50, 50)"/>
101 <has_line line="Writing 25 image(s)"/> 118 <has_line line="Writing 5 out of 25 image(s)"/>
102 <has_line line="Output axes: ZCYX"/> 119 <has_line line="Output axes: ZCYX"/>
103 <has_line line="Output shape: (1, 2, 50, 50)"/> 120 <has_line line="Output shape: (1, 2, 50, 50)"/>
104 </assert_stdout> 121 </assert_stdout>
105 </test> 122 </test>
106 <test> 123 <test>
112 <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/> 129 <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/>
113 </output_collection> 130 </output_collection>
114 <assert_stdout> 131 <assert_stdout>
115 <has_line line="Input image axes: QYX"/> 132 <has_line line="Input image axes: QYX"/>
116 <has_line line="Input image shape: (2, 256, 256)"/> 133 <has_line line="Input image shape: (2, 256, 256)"/>
117 <has_line line="Writing 2 image(s)"/> 134 <has_line line="Writing 2 out of 2 image(s)"/>
118 <has_line line="Output axes: QYX"/> 135 <has_line line="Output axes: QYX"/>
119 <has_line line="Output shape: (1, 256, 256)"/> 136 <has_line line="Output shape: (1, 256, 256)"/>
120 </assert_stdout> 137 </assert_stdout>
121 </test> 138 </test>
122 <test> 139 <test>
125 <param name="squeeze" value="false" /> 142 <param name="squeeze" value="false" />
126 <output_collection name="output" type="list" count="1"> 143 <output_collection name="output" type="list" count="1">
127 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/> 144 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/>
128 </output_collection> 145 </output_collection>
129 <assert_stdout> 146 <assert_stdout>
130 <has_line line="Found TIFF with 1 series"/> 147 <has_line line="Found 1 image(s) in file"/>
131 </assert_stdout> 148 </assert_stdout>
132 </test> 149 </test>
133 150
134 <!-- Test splitting multi-series TIFF --> 151 <!-- Test splitting multi-series TIFF -->
135 <test> 152 <test>
139 <output_collection name="output" type="list" count="6"> 156 <output_collection name="output" type="list" count="6">
140 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/> 157 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/>
141 <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/> 158 <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/>
142 </output_collection> 159 </output_collection>
143 <assert_stdout> 160 <assert_stdout>
144 <has_line line="Found TIFF with 6 series"/> 161 <has_line line="Found 6 image(s) in file"/>
145 <has_line line="Writing 6 image(s)"/> 162 <has_line line="Writing 6 out of 6 image(s)"/>
146 <has_line line="Output 1 axes: CYX"/> 163 <has_line line="Output 1 axes: CYX"/>
147 <has_line line="Output 1 shape: (4, 5, 5)"/> 164 <has_line line="Output 1 shape: (4, 5, 5)"/>
148 <has_line line="Output 2 axes: CYX"/> 165 <has_line line="Output 2 axes: CYX"/>
149 <has_line line="Output 2 shape: (4, 5, 5)"/> 166 <has_line line="Output 2 shape: (4, 5, 5)"/>
150 <has_line line="Output 3 axes: CYX"/> 167 <has_line line="Output 3 axes: CYX"/>
169 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/> 186 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/>
170 </output_collection> 187 </output_collection>
171 <assert_stdout> 188 <assert_stdout>
172 <has_line line="Input image axes: YXC"/> 189 <has_line line="Input image axes: YXC"/>
173 <has_line line="Input image shape: (32, 32, 3)"/> 190 <has_line line="Input image shape: (32, 32, 3)"/>
174 <has_line line="Writing 3 image(s)"/> 191 <has_line line="Writing 3 out of 3 image(s)"/>
175 <has_line line="Output axes: YX"/> 192 <has_line line="Output axes: YX"/>
176 <has_line line="Output shape: (32, 32)"/> 193 <has_line line="Output shape: (32, 32)"/>
177 </assert_stdout> 194 </assert_stdout>
178 </test> 195 </test>
179 196
186 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/> 203 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/>
187 </output_collection> 204 </output_collection>
188 <assert_stdout> 205 <assert_stdout>
189 <has_line line="Input image axes: YXC"/> 206 <has_line line="Input image axes: YXC"/>
190 <has_line line="Input image shape: (32, 32, 3)"/> 207 <has_line line="Input image shape: (32, 32, 3)"/>
191 <has_line line="Writing 1 image(s)"/> 208 <has_line line="Writing 1 out of 1 image(s)"/>
192 <has_line line="Output axes: YXC"/> 209 <has_line line="Output axes: YXC"/>
193 <has_line line="Output shape: (32, 32, 3)"/> 210 <has_line line="Output shape: (32, 32, 3)"/>
194 </assert_stdout> 211 </assert_stdout>
195 </test> 212 </test>
196 213