Mercurial > repos > bgruening > cp_measure_image_intensity
comparison starting_modules_nameandtypes.xml @ 3:2681008d726f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
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date | Mon, 11 May 2020 07:52:05 -0400 |
parents | |
children | 8536b1ae0254 |
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2:20525bc7f6f4 | 3:2681008d726f |
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1 <macros> | |
2 <xml name="macro_image_type" token_thing="images"> | |
3 <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" /> | |
4 </xml> | |
5 | |
6 <xml name="image_type_condition"> | |
7 <conditional name="con_set_intensity"> | |
8 <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0."> | |
9 <option value="Image metadata">Image metadata</option> | |
10 <option value="Image bit-depth">Image bit-depth</option> | |
11 <option value="Manual">Manual</option> | |
12 </param> | |
13 <when value="Manual"> | |
14 <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." /> | |
15 | |
16 </when> | |
17 <when value="Image metadata" /> | |
18 <when value="Image bit-depth" /> | |
19 </conditional> | |
20 </xml> | |
21 <xml name="name_type_rule_matching_file"> | |
22 <param name="operator" type="select"> | |
23 <option value="does">Does</option> | |
24 <option value="doesnot">Does not</option> | |
25 </param> | |
26 <param name="contain" type="select"> | |
27 <option value="contain">Contain</option> | |
28 <option value="Contain regular expression">Contain regular expression</option> | |
29 <option value="startwith">Start with</option> | |
30 <option value="endwith">End with</option> | |
31 <option value="Exactly match">Exactly match</option> | |
32 </param> | |
33 <param name="match_value" type="text"/> | |
34 </xml> | |
35 <xml name="name_type_rule_image"> | |
36 <param name="operator" type="select"> | |
37 <option value="does">Is</option> | |
38 <option value="doesnot">Is not</option> | |
39 </param> | |
40 <param name="match_type" type="select"> | |
41 <option value="iscolor">Color</option> | |
42 <option value="ismonochrome">Monochrome</option> | |
43 <option value="isstack">Stack</option> | |
44 <option value="isstackframe">Stack frame</option> | |
45 </param> | |
46 </xml> | |
47 <xml name="name_type_rule_metadata"> | |
48 <param name="operator" type="select"> | |
49 <option value="does">Does</option> | |
50 <option value="doesnot">Does not</option> | |
51 </param> | |
52 <param name="match_type" type="select"> | |
53 <option value="FileLocation">Have FileLocation matching</option> | |
54 <option value="Frame">Have Frame matching</option> | |
55 <option value="Screen">Have Screen matching</option> | |
56 <option value="Series">Have Series matching</option> | |
57 </param> | |
58 <param name="match_value" type="text"/> | |
59 </xml> | |
60 <xml name="name_type_rule_ext"> | |
61 <param name="operator" type="select"> | |
62 <option value="does">Is</option> | |
63 <option value="doesnot">Is not</option> | |
64 </param> | |
65 <param name="match_type" type="select"> | |
66 <option value="istif">tif, tiff, ome.tif or ome.tiff</option> | |
67 <option value="isjpeg">jpg, jpeg</option> | |
68 <option value="ispng">png</option> | |
69 <option value="isimage">the extension of an image file</option> | |
70 <option value="isflex">flex</option> | |
71 <option value="ismovie">mov, avi</option> | |
72 | |
73 </param> | |
74 </xml> | |
75 <xml name="image_matching_rules"> | |
76 <repeat name="r_match_rule" title="Another image"> | |
77 <param name="match_all_any" type="select" display="radio" label="Match the following rules"> | |
78 <option value="and">All</option> | |
79 <option value="or">Any</option> | |
80 </param> | |
81 <repeat name="r_match" title="rule"> | |
82 <conditional name="con_match"> | |
83 <param name="rule_type" type="select" label="Select rule criteria"> | |
84 <option value="file">File</option> | |
85 <option value="directory">Directory</option> | |
86 <option value="extension">Extension</option> | |
87 <option value="image">Image</option> | |
88 <option value="metadata">Metadata</option> | |
89 </param> | |
90 <when value="file"> | |
91 <expand macro="name_type_rule_matching_file"/> | |
92 </when> | |
93 <when value="directory"> | |
94 <expand macro="name_type_rule_matching_file"/> | |
95 </when> | |
96 <when value="extension"> | |
97 <expand macro="name_type_rule_ext" /> | |
98 </when> | |
99 <when value="image"> | |
100 <expand macro="name_type_rule_image" /> | |
101 </when> | |
102 <when value="metadata"> | |
103 <expand macro="name_type_rule_metadata" /> | |
104 </when> | |
105 </conditional> | |
106 </repeat> | |
107 <conditional name="con_select_image_type"> | |
108 <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated"> | |
109 <option value="Grayscale image">Grayscale image</option> | |
110 <option value="Color image">Color image</option> | |
111 <option value="Binary mask">Binary mask</option> | |
112 <option value="Illumination function">Illumination function</option> | |
113 <option value="Objects">Objects</option> | |
114 | |
115 </param> | |
116 <when value ="Grayscale image"> | |
117 <expand macro="macro_image_type" thing="images"/> | |
118 <expand macro="image_type_condition" /> | |
119 </when> | |
120 <when value="Color image"> | |
121 <expand macro="macro_image_type" thing="images"/> | |
122 <expand macro="image_type_condition" /> | |
123 </when> | |
124 <when value="Binary mask"> | |
125 <expand macro="macro_image_type" thing="images"/> | |
126 </when> | |
127 <when value="Illumination function"> | |
128 <expand macro="macro_image_type" thing="images"/> | |
129 </when> | |
130 <when value="Objects"> | |
131 <expand macro="macro_image_type" thing="objects"/> | |
132 </when> | |
133 </conditional> | |
134 </repeat> | |
135 </xml> | |
136 <xml name="starting_modules_nameandtypes"> | |
137 <section name="nameandtypes" title="NamesAndTypes" expanded="false"> | |
138 <conditional name="pixel_space"> | |
139 <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images."> | |
140 <option value="Yes">Yes, process 3D data</option> | |
141 <option value="No">No, do not process 3D data</option> | |
142 </param> | |
143 <when value="Yes"> | |
144 <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." /> | |
145 <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/> | |
146 <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/> | |
147 </when> | |
148 <when value="No"/> | |
149 </conditional> | |
150 <conditional name="con_assign_a_name_to"> | |
151 <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools."> | |
152 <option value="All images">Give every image the same name</option> | |
153 <option value="Images matching rules">Give images one of several names depending on the metadata</option> | |
154 </param> | |
155 <when value="All images"> | |
156 <expand macro="macro_image_type" thing="images" /> | |
157 <conditional name="con_select_image_type"> | |
158 <param name="select_image_type" type="select" label="Select the image type"> | |
159 <option value="Grayscale image">Grayscale image</option> | |
160 <option value="Color image">Color image</option> | |
161 <option value="Binary mask">Binary mask</option> | |
162 </param> | |
163 <when value ="Grayscale image"> | |
164 <expand macro="image_type_condition" /> | |
165 </when> | |
166 <when value="Color image"> | |
167 <expand macro="image_type_condition" /> | |
168 </when> | |
169 <when value="Binary mask" /> | |
170 </conditional> | |
171 </when> | |
172 <when value="Images matching rules"> | |
173 <expand macro="image_matching_rules"/> | |
174 <param name="matching_method" type="select" label="Image set matching method"> | |
175 <option value="Order">Order</option> | |
176 <option value="Metadata">Metadata</option> | |
177 </param> | |
178 </when> | |
179 </conditional> | |
180 </section> | |
181 </xml> | |
182 </macros> |