Mercurial > repos > bgruening > cp_save_images

comparison save_images.xml @ 0:6e0f244acd32 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 17:42:45 -0400
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children 609911f19ab2
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-1:000000000000 0:6e0f244acd32
1 <tool id="cp_save_images" name="SaveImages" version="@CP_VERSION@">
2 <description>saves image or movie files</description>
3
4 <macros>
5 <import>macros.xml</import>
6 <xml name="file_format">
7 <param name="file_format" label="Saved file format" type="select">
8 <option value="jpeg">jpeg</option>
9 <option value="npy">npy</option>
10 <option value="png">png</option>
11 <option value="tiff">tiff</option>
12 </param>
13 </xml>
14 <xml name="bit_depth">
15 <param name="bit_depth" label="Image bit depth" type="select">
16 <option value="8-bit integer">8-bit integer</option>
17 <option value="16-bit integer">16-bit integer</option>
18 <option value="32-bit floating point">32-bit floating point</option>
19 </param>
20 </xml>
21 </macros>
22
23 <expand macro="py_requirements"/>
24 <expand macro="cmd_modules" />
25
26 <configfiles>
27 <inputs name="inputs" />
28 <configfile name="script_file">
29 import json
30 import sys
31 import os
32
33 FOURSPACES=@SPACES@
34
35 input_json_path = sys.argv[1]
36 input_pipeline= sys.argv[2]
37
38 params = json.load(open(input_json_path, "r"))
39
40 def writesi():
41 _str = "\nSaveImages:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
42
43 _str += FOURSPACES + "Select the type of image to save:%s\n" % params['con_type_of_image']['type_of_image']
44
45 _str += FOURSPACES + "Select the image to save:%s\n" % params['image_to_save']
46
47 method_for_constructing = params['con_method_for_constructing']['method_for_constructing']
48 _str += FOURSPACES + "Select method for constructing file names:%s\n" % method_for_constructing
49
50 if method_for_constructing == "From image filename":
51 img_name_file_prefix = params['con_method_for_constructing']['name_for_file_prefix']
52 append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
53
54 if append_suffix == "Yes":
55 text_append = params['con_method_for_constructing']['con_append_suffix']['text_to_append']
56 else:
57 text_append = ""
58 else:
59 img_name_file_prefix = "None"
60 append_suffix = "No"
61 text_append = ""
62
63 _str += FOURSPACES + "Select image name for file prefix:%s\n" % img_name_file_prefix
64
65 if method_for_constructing == "Sequential numbers":
66 file_prefix = params['con_method_for_constructing']['file_prefix']
67 no_of_digits = params['con_method_for_constructing']['no_of_digits']
68
69 _str += FOURSPACES + "Enter file prefix:%s\n" % file_prefix
70 elif method_for_constructing == "Single name":
71 _str += FOURSPACES + "Enter single file name:%s\n" % params['con_method_for_constructing'][
72 'single_file_name']
73
74 no_of_digits = 4
75 else:
76 _str += FOURSPACES + "Enter single file name:OrigBlue\n"
77 no_of_digits = 4
78 append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
79
80 _str += FOURSPACES + "Number of digits:%d\n" % no_of_digits
81 _str += FOURSPACES + "Append a suffix to the image file name?:%s\n" % append_suffix
82 _str += FOURSPACES + "Text to append to the image name:%s\n" % text_append
83
84 save_format = params['con_type_of_image']['con_save_file_format']['file_format']
85
86 _str += FOURSPACES + "Saved file format:%s\n" % save_format
87
88 if save_format == "tiff":
89 bit_depth = params['con_type_of_image']['con_save_file_format']['bit_depth']
90 else:
91 bit_depth = "8-bit integer"
92
93 _str += FOURSPACES + "Output file location:Default Output Folder\\x7Coutput\n"
94 _str += FOURSPACES + "Image bit depth:%s\n" % bit_depth
95 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params['overwrite_without_warning']
96 _str += FOURSPACES + "When to save:%s\n" % params['when_to_save']
97 _str += FOURSPACES + "Record the file and path information to the saved image?:%s\n" % params['record_info']
98 _str += FOURSPACES + "Create subfolders in the output folder?:%s\n" % params['subfolder_in_output']
99 _str += FOURSPACES + "Base image folder:Elsewhere...\n"
100
101 return _str
102
103 with open(input_pipeline) as fin:
104 lines = fin.readlines()
105
106 k, v = lines[4].strip().split(':')
107
108 module_count = int(v)
109 new_count = module_count + 1
110 lines[4] = k + ":%d\n" % new_count
111
112 with open("output", "w") as f:
113 f.writelines(lines)
114 f.write(writesi())
115
116 f.close()
117 </configfile>
118 </configfiles>
119
120 <inputs>
121 <expand macro="input_pipeline_macro" />
122 <conditional name="con_type_of_image">
123 <param name="type_of_image" type="select" label="Select the type of image to save" >
124 <option value="Image">Image</option>
125 <option value="Mask">Mask</option>
126 <option value="Cropping">Cropping</option>
127 <option value="Movie">Movie</option>
128 </param>
129 <when value="Image">
130 <conditional name="con_save_file_format">
131 <expand macro="file_format" />
132 <when value="tiff">
133 <expand macro="bit_depth" />
134 </when>
135 <when value="jpeg" />
136 <when value="npy" />
137 <when value="png" />
138 </conditional>
139 </when>
140 <when value="Mask">
141 <expand macro="file_format" />
142 </when>
143 <when value="Cropping">
144 <expand macro="file_format" />
145 </when>
146 <when value="Movie">
147 <expand macro="bit_depth" />
148 </when>
149 </conditional>
150 <param name="image_to_save" label="Select the image to save" type="text" />
151 <conditional name="con_method_for_constructing">
152 <param name="method_for_constructing" label="Select method for constructing file names" type="select" >
153 <option value="From image filename">From image filename</option>
154 <option value="Sequential numbers">Sequential numbers</option>
155 <option value="Single name">Single name</option>
156 </param>
157 <when value="From image filename">
158 <param name="name_for_file_prefix" label="Select image name for file prefix" type="text">
159 <expand macro="text_validator" />
160 </param>
161 <conditional name="con_append_suffix">
162 <param name="append_suffix" type="select" display="radio" label="Append a suffix to the image file name?">
163 <option value="No">No</option>
164 <option value="Yes">Yes</option>
165 </param>
166 <when value="Yes">
167 <param name="text_to_append" label="Text to append to the image name" type="text">
168 <expand macro="text_validator" />
169 </param>
170 </when>
171 <when value="No" />
172 </conditional>
173 </when>
174 <when value="Sequential numbers">
175 <param name="file_prefix" label="Enter file prefix" type="text"/>
176 <param name="no_of_digits" label="Number of digits" type="integer" value="4" min="0"/>
177 </when>
178 <when value="Single name">
179 <param name="single_file_name" label="Enter single_file_name" type="text">
180 <expand macro="text_validator" />
181 </param>
182 </when>
183 </conditional>
184 <param name="overwrite_without_warning" label="Overwrite existing files without warning?" type="select" >
185 <option value="No">No</option>
186 <option value="Yes">Yes</option>
187 </param>
188 <param name="when_to_save" label="When to save" type="select" >
189 <option value="Every cycle">Every cycle</option>
190 <option value="First cycle">First cycle</option>
191 <option value="Last cycle">Last cycle</option>
192 </param>
193 <param name="record_info" label="Record the file and path information to the saved image?" type="select" display="radio">
194 <option value="No">No</option>
195 <option value="Yes">Yes</option>
196 </param>
197 <param name="subfolder_in_output" label="Create subfolders in the output folder?" type="select" display="radio">
198 <option value="No">No</option>
199 </param>
200 </inputs>
201
202 <outputs>
203 <expand macro="output_pipeline_macro" />
204 </outputs>
205
206 <tests>
207 <test>
208 <expand macro="test_input_pipeline_param" />
209
210 <conditional name="con_type_of_image">
211 <param name="type_of_image" value="Image" />
212 <conditional name="con_save_file_format">
213 <param name="file_format" value="tiff" />
214 <param name="bit_depth" value="8-bit integer" />
215 </conditional>
216 </conditional>
217 <param name="image_to_save" value="ImageDisplay" />
218 <conditional name="con_method_for_constructing" >
219 <param name="method_for_constructing" value="From image filename" />
220 <param name="name_for_file_prefix" value="DNA" />
221 <conditional name="con_append_suffix">
222 <param name="append_suffix" value="Yes" />
223 <param name="text_to_append" value="_nucleiNumbers" />
224 </conditional>
225 </conditional>
226 <param name="overwrite_without_warning" value="Yes" />
227 <param name="when_to_save" value="Every cycle" />
228 <param name="record_info" value="No" />
229 <param name="subfolder_in_output" value="No" />
230
231 <expand macro="test_out_file" file="save_images.txt" />
232
233 </test>
234 </tests>
235
236 <expand macro="help" module="RelateObjects" />
237 <expand macro="citations" />
238
239 </tool>