comparison starting_modules_nameandtypes.xml @ 0:4395ea2a01f4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:00:10 +0000
parents
children e8f822eeb9fd
comparison
equal deleted inserted replaced
-1:000000000000 0:4395ea2a01f4
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>