Mercurial > repos > bgruening > vpt_extract

comparison macros.xml @ 0:e08b21abb96d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
author bgruening
date Sun, 22 Jun 2025 12:25:39 +0000
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-1:000000000000 0:e08b21abb96d
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.0</token>
3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@PROFILE@">23.0</token>
5 <xml name="requirements">
6 <requirements>
7 <container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
8 <yield/>
9 </requirements>
10 </xml>
11 <xml name="creator">
12 <creator>
13 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
14 <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
15 <person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
16 <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
17 </creator>
18 </xml>
19 <token name="@CMD@"><![CDATA[
20 mkdir -p 'input/images' 'output/' &&
21 #for $image in $input_images:
22 ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
23 #end for
24 ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
25 ]]></token>
26 <token name="@COMMON_ARGS@"><![CDATA[
27 --processes \${GALAXY_SLOTS:-10}
28 --verbose
29 --log-file 'output/log'
30 ]]>
31 </token>
32 <xml name="common_input">
33 <param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
34 <param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
35 </xml>
36 <xml name="normalization_param" token_label="Normalization">
37 <param name="normalization" type="select" label="@LABEL@">
38 <option value="default">default (min-max range normalization)</option>
39 <option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
40 </param>
41 </xml>
42 <xml name="channel_options_basic">
43 <yield/>
44 <option value="Cellbound1">Cellbound1</option>
45 <option value="Cellbound2">Cellbound2</option>
46 <option value="Cellbound3">Cellbound3</option>
47 </xml>
48 <xml name="channel_options_none">
49 <expand macro="channel_options_basic">
50 <option value="None" selected="true">None</option>
51 <option value="DAPI">DAPI</option>
52 <option value="PolyT">PolyT</option>
53 <yield/>
54 </expand>
55 </xml>
56 <xml name="advanced_output">
57 <section name="advanced_output" title="Advanced output options">
58 <param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
59 </section>
60 </xml>
61 <xml name="common_output">
62 <data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
63 <filter>advanced_output['log']</filter>
64 </data>
65 </xml>
66 <xml name="task_input_data">
67 <conditional name="normalize_conditional">
68 <param name="normalize_select" type="select" label="Perform Normalization?">
69 <option value="Yes" selected="true">Yes</option>
70 <option value="No">No</option>
71 </param>
72 <when value="Yes">
73 <conditional name="normalize_type_conditional" label="Select normalization method">
74 <expand macro="normalization_param"/>
75 <when value="default"/>
76 <when value="CLAHE">
77 <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
78 <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
79 </when>
80 </conditional>
81 </when>
82 <when value="No"/>
83 </conditional>
84 <conditional name="blur_conditional">
85 <param name="blur_select" type="select" label="Perform Blur?">
86 <option value="Yes">Yes</option>
87 <option value="No" selected="true">No</option>
88 </param>
89 <when value="Yes">
90 <param name="blur_options" type="select" label="Blur options">
91 <option value="average">average</option>
92 <option value="median">median</option>
93 <option value="gaussian">gaussian</option>
94 </param>
95 <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
96 </when>
97 <when value="No"/>
98 </conditional>
99 <conditional name="downsample_conditional">
100 <param name="downsample_select" type="select" label="Perform downsample?">
101 <option value="Yes">Yes</option>
102 <option value="No" selected="true">No</option>
103 </param>
104 <when value="Yes">
105 <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
106 </when>
107 <when value="No"/>
108 </conditional>
109 </xml>
110 <xml name="channel_map_conditional_childs">
111 <when value="None"/>
112 <when value="DAPI">
113 <expand macro="task_input_data"/>
114 </when>
115 <when value="PolyT">
116 <expand macro="task_input_data"/>
117 </when>
118 <when value="Cellbound1">
119 <expand macro="task_input_data"/>
120 </when>
121 <when value="Cellbound2">
122 <expand macro="task_input_data"/>
123 </when>
124 <when value="Cellbound3">
125 <expand macro="task_input_data"/>
126 </when>
127 </xml>
128 <xml name="sanitize_digits">
129 <sanitizer invalid_char="">
130 <valid initial="string.digits">
131 <add value=","/>
132 <add value="."/>
133 </valid>
134 </sanitizer>
135 </xml>
136 <xml name="citations">
137 <citations>
138 <citation type="bibtex">@Manual{github,
139 title = {Vizgen Post-processing Tool},
140 author = {Vizgen},
141 organization = {Vizgen},
142 year = {2022},
143 url = {https://github.com/Vizgen/vizgen-postprocessing}}
144 </citation>
145 </citations>
146 </xml>
147 </macros>