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comparison clip_image.xml @ 1:eb5a84e77beb draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
author imgteam
date Sun, 04 Jan 2026 22:20:07 +0000
parents 969840610383
children
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0:969840610383 1:eb5a84e77beb
1 <tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1">
2 <description>with giatools</description> 2 <description>with giatools</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@">0.7.3</token> 6 <token name="@TOOL_VERSION@">0.7.3</token>
7 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
8 <xml name="bound" tokens="name,label,help"> 8 <xml name="bound" tokens="name,label,help">
9 <param name="@NAME@" type="float" label="@LABEL@" help="@HELP@"/> 9 <param name="@NAME@" type="float" optional="true" label="@LABEL@" help="@HELP@"/>
10 </xml>
11 <xml name="lower_bound">
12 <expand macro="bound" name="lower_bound" label="Lower bound"
13 help="Image intensities below this value will be set to this value."/>
14 </xml>
15 <xml name="upper_bound">
16 <expand macro="bound" name="upper_bound" label="Upper bound"
17 help="Image intensities above this value will be set to this value."/>
18 </xml> 10 </xml>
19 </macros> 11 </macros>
20 <creator> 12 <creator>
21 <expand macro="creators/bmcv"/> 13 <expand macro="creators/bmcv"/>
22 <expand macro="creators/kostrykin"/> 14 <expand macro="creators/kostrykin"/>
53 ]]></command> 45 ]]></command>
54 <configfiles> 46 <configfiles>
55 <configfile name="params"><![CDATA[ 47 <configfile name="params"><![CDATA[
56 { 48 {
57 49
58 #if "lower" in str($setup.mode) 50 #if str($lower_bound) != ""
59 "lower_bound": $setup.lower_bound, 51 "lower_bound": $lower_bound,
60 #end if 52 #end if
61 53
62 #if "upper" in str($setup.mode) 54 #if str($upper_bound) != ""
63 "upper_bound": $setup.upper_bound, 55 "upper_bound": $upper_bound,
64 #end if 56 #end if
65 57
66 "": null 58 "": null
67 } 59 }
68 ]]></configfile> 60 ]]></configfile>
69 </configfiles> 61 </configfiles>
70 <inputs> 62 <inputs>
71 <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/> 63 <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/>
72 <conditional name="setup"> 64 <expand macro="bound" name="lower_bound" label="Lower bound"
73 <param name="mode" type="select" label="Clipping"> 65 help="Image intensities below this value will be set to this value."/>
74 <option value="lower-upper" selected="true">Clip to lower and upper bounds</option> 66 <expand macro="bound" name="upper_bound" label="Upper bound"
75 <option value="lower">Clip to lower bound</option> 67 help="Image intensities above this value will be set to this value."/>
76 <option value="upper">Clip to upper bound</option>
77 </param>
78 <when value="lower-upper">
79 <expand macro="lower_bound"/>
80 <expand macro="upper_bound"/>
81 </when>
82 <when value="lower">
83 <expand macro="lower_bound"/>
84 </when>
85 <when value="upper">
86 <expand macro="upper_bound"/>
87 </when>
88 </conditional>
89 </inputs> 68 </inputs>
90 <outputs> 69 <outputs>
91 <data format="tiff" name="output" from_work_dir="output.tiff"/> 70 <data format="tiff" name="output" from_work_dir="output.tiff"/>
92 </outputs> 71 </outputs>
93 <tests> 72 <tests>
94 <test> 73 <test>
95 <param name="input" value="input/input4_float16.tiff"/> 74 <param name="input" value="input/input4_float16.tiff"/>
96 <conditional name="setup"> 75 <param name="lower_bound" value="0.5"/>
97 <param name="mode" value="lower"/>
98 <param name="lower_bound" value="0.5"/>
99 </conditional>
100 <expand macro="tests/intensity_image_diff" name="output" value="output/input4.tiff" ftype="tiff"/> 76 <expand macro="tests/intensity_image_diff" name="output" value="output/input4.tiff" ftype="tiff"/>
101 <assert_stdout> 77 <assert_stdout>
102 <has_line line="[input] Input image axes: ZYX"/> 78 <has_line line="[input] Input image axes: ZYX"/>
103 <has_line line="[input] Input image shape: (10, 15, 18)"/> 79 <has_line line="[input] Input image shape: (10, 15, 18)"/>
104 <has_line line="[input] Input image dtype: float16"/> 80 <has_line line="[input] Input image dtype: float16"/>
110 <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/> 86 <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
111 </assert_stdout> 87 </assert_stdout>
112 </test> 88 </test>
113 <test> 89 <test>
114 <param name="input" value="input/input5.jpg"/> 90 <param name="input" value="input/input5.jpg"/>
115 <conditional name="setup"> 91 <param name="upper_bound" value="100.5"/>
116 <param name="mode" value="upper"/>
117 <param name="upper_bound" value="100.5"/>
118 </conditional>
119 <expand macro="tests/intensity_image_diff" name="output" value="output/input5.tiff" ftype="tiff"/> 92 <expand macro="tests/intensity_image_diff" name="output" value="output/input5.tiff" ftype="tiff"/>
120 <assert_stdout> 93 <assert_stdout>
121 <has_line line="[input] Input image axes: YXC"/> 94 <has_line line="[input] Input image axes: YXC"/>
122 <has_line line="[input] Input image shape: (10, 10, 3)"/> 95 <has_line line="[input] Input image shape: (10, 10, 3)"/>
123 <has_line line="[input] Input image dtype: uint8"/> 96 <has_line line="[input] Input image dtype: uint8"/>
127 <has_line line="[output] Output image dtype: uint8"/> 100 <has_line line="[output] Output image dtype: uint8"/>
128 </assert_stdout> 101 </assert_stdout>
129 </test> 102 </test>
130 <test expect_failure="true"> 103 <test expect_failure="true">
131 <param name="input" value="input/input5.jpg"/> 104 <param name="input" value="input/input5.jpg"/>
132 <conditional name="setup"> 105 <param name="lower_bound" value="60"/>
133 <param name="mode" value="lower-upper"/> 106 <param name="upper_bound" value="50"/>
134 <param name="lower_bound" value="60"/>
135 <param name="upper_bound" value="50"/>
136 </conditional>
137 <assert_stderr> 107 <assert_stderr>
138 <has_line line="Lower bound (60) must be less or equal compared to the upper bound (50)."/> 108 <has_line line="Lower bound (60) must be less or equal compared to the upper bound (50)."/>
139 </assert_stderr> 109 </assert_stderr>
140 </test> 110 </test>
141 <test> 111 <test>
142 <param name="input" value="input/input6_yx.zarr"/> 112 <param name="input" value="input/input6_yx.zarr"/>
143 <conditional name="setup"> 113 <param name="lower_bound" value="-21.5"/>
144 <param name="mode" value="lower-upper"/> 114 <param name="upper_bound" value="101.5"/>
145 <param name="lower_bound" value="-21.5"/>
146 <param name="upper_bound" value="101.5"/>
147 </conditional>
148 <expand macro="tests/intensity_image_diff" name="output" value="output/input6.tiff" ftype="tiff"/> 115 <expand macro="tests/intensity_image_diff" name="output" value="output/input6.tiff" ftype="tiff"/>
149 <assert_stdout> 116 <assert_stdout>
150 <has_line line="[input] Input image axes: YX"/> 117 <has_line line="[input] Input image axes: YX"/>
151 <has_line line="[input] Input image shape: (200, 200)"/> 118 <has_line line="[input] Input image shape: (200, 200)"/>
152 <has_line line="[input] Input image dtype: float64"/> 119 <has_line line="[input] Input image dtype: float64"/>
154 <has_line line="Applying clipping: [-21.5, 101.5]"/> 121 <has_line line="Applying clipping: [-21.5, 101.5]"/>
155 <has_line line="[output] Output image axes: YX"/> 122 <has_line line="[output] Output image axes: YX"/>
156 <has_line line="[output] Output image shape: (200, 200)"/> 123 <has_line line="[output] Output image shape: (200, 200)"/>
157 <has_line line="[output] Output image dtype: float64"/> 124 <has_line line="[output] Output image dtype: float64"/>
158 <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um'"/> 125 <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um'"/>
126 </assert_stdout>
127 </test>
128 <test>
129 <param name="input" value="input/input4_float16.tiff"/>
130 <expand macro="tests/intensity_image_diff" name="output" value="input/input4_float16.tiff" ftype="tiff"/>
131 <assert_stdout>
132 <has_line line="[input] Input image axes: ZYX"/>
133 <has_line line="[input] Input image shape: (10, 15, 18)"/>
134 <has_line line="[input] Input image dtype: float16"/>
135 <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
136 <has_line line="Applying clipping: [-inf, inf]"/>
137 <has_line line="[output] Output image axes: ZYX"/>
138 <has_line line="[output] Output image shape: (10, 15, 18)"/>
139 <has_line line="[output] Output image dtype: float16"/>
140 <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
159 </assert_stdout> 141 </assert_stdout>
160 </test> 142 </test>
161 </tests> 143 </tests>
162 <help> 144 <help>
163 145