Mercurial > repos > bgruening > cp_convert_objects_to_image
comparison convert_objects_to_image.xml @ 0:d9fa2e6fae97 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author | bgruening |
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date | Thu, 26 Mar 2020 16:17:05 -0400 |
parents | |
children | 1221c018f7be |
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-1:000000000000 | 0:d9fa2e6fae97 |
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1 <tool id="cp_convert_objects_to_image" name="ConvertObjectsToImage" version="@CP_VERSION@"> | |
2 <description>converts the identified objects into an image</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="py_requirements"/> | |
7 <expand macro="cmd_modules" /> | |
8 <configfiles> | |
9 <inputs name="inputs" /> | |
10 <configfile name="script_file"> | |
11 import json | |
12 import sys | |
13 import os | |
14 | |
15 FOURSPACES=@SPACES@ | |
16 | |
17 input_json_path = sys.argv[1] | |
18 input_pipeline= sys.argv[2] | |
19 | |
20 params = json.load(open(input_json_path, "r")) | |
21 | |
22 | |
23 def writecoti(): | |
24 _str = "\nConvertObjectsToImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count | |
25 | |
26 _str += FOURSPACES + "Select the input objects:%s\n" % params['input_object'] | |
27 _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image'] | |
28 | |
29 color_format = params['con_color_format']['color_format'] | |
30 | |
31 _str += FOURSPACES + "Select the color format:%s\n" % color_format | |
32 | |
33 if color_format == "Color": | |
34 _str += FOURSPACES + "Select the colormap:%s\n" % params['con_color_format']['color_map'] | |
35 else: | |
36 _str += FOURSPACES + "Select the colormap:Default\n" | |
37 | |
38 return _str | |
39 | |
40 | |
41 with open(input_pipeline) as fin: | |
42 lines = fin.readlines() | |
43 k, v = lines[4].strip().split(':') | |
44 | |
45 module_count = int(v) | |
46 new_count = module_count + 1 | |
47 lines[4] = k + ":%d\n" % new_count | |
48 with open("output", "w") as f: | |
49 f.writelines(lines) | |
50 f.write(writecoti()) | |
51 | |
52 f.close() | |
53 </configfile> | |
54 </configfiles> | |
55 | |
56 <inputs> | |
57 <expand macro="input_pipeline_macro" /> | |
58 <param name="input_object" type="text" label="Select the input objects" /> | |
59 <param name="name_output_image" type="text" label="Name the output image"> | |
60 <expand macro="text_validator" /> | |
61 </param> | |
62 | |
63 <conditional name="con_color_format"> | |
64 <param name="color_format" type="select" label="Select the color format"> | |
65 <option value="Color">Color</option> | |
66 <option value="Binary (black & white)">Binary (black & white)</option> | |
67 <option value="Grayscale">Grayscale</option> | |
68 <option value="unit16">unit16</option> | |
69 <sanitizer sanitize="false"/> | |
70 </param> | |
71 <when value="Binary (black & white)" /> | |
72 <when value="Grayscale" /> | |
73 <when value="unit16" /> | |
74 <when value="Color"> | |
75 <param name="color_map" type="select" label="Select the colormap"> | |
76 <option value="Default">Default</option> | |
77 <option value="Accent">Accent</option> | |
78 <option value="Blues">Blues</option> | |
79 <option value="BrBG">BrBG</option> | |
80 <option value="BuGn">BuGn</option> | |
81 <option value="BuPu">BuPu</option> | |
82 <option value="Dark2">Dark2</option> | |
83 <option value="GnBu">GnBu</option> | |
84 <option value="Greens">Greens</option> | |
85 <option value="Greys">Greys</option> | |
86 <option value="OrRd">OrRd</option> | |
87 <option value="Oranges">Oranges</option> | |
88 <option value="PRGn">PRGn</option> | |
89 <option value="Paired">Paired</option> | |
90 <option value="Pastel1">Pastel1</option> | |
91 <option value="Pastel2">Pastel2</option> | |
92 <option value="PiYG">PiYG</option> | |
93 <option value="PuBu">PuBu</option> | |
94 <option value="PuBuGn">PuBuGn</option> | |
95 <option value="PuOr">PuOr</option> | |
96 <option value="PuRd">PuRd</option> | |
97 <option value="Purples">Purples</option> | |
98 <option value="RdBu">RdBu</option> | |
99 <option value="RdGy">RdGy</option> | |
100 <option value="RdPu">RdPu</option> | |
101 <option value="RdYIBu">RdYIBu</option> | |
102 <option value="RdYiGn">RdYiGn</option> | |
103 <option value="Reds">Reds</option> | |
104 <option value="Set1">Set1</option> | |
105 <option value="Set2">Set2</option> | |
106 <option value="Set3">Set3</option> | |
107 <option value="Spectral">Spectral</option> | |
108 <option value="YIGn">YIGn</option> | |
109 <option value="YIGnBu">YIGnBu</option> | |
110 <option value="YIOrBr">YIOrBr</option> | |
111 <option value="YIOrRd">YIOrRd</option> | |
112 <option value="autumn">autumn</option> | |
113 <option value="binary">binary</option> | |
114 <option value="bone">bone</option> | |
115 <option value="cool">cool</option> | |
116 <option value="copper">copper</option> | |
117 <option value="flag">flag</option> | |
118 <option value="gist_earth">gist_earth</option> | |
119 <option value="gist_gray">gist_gray</option> | |
120 <option value="gist_heat">gist_heat</option> | |
121 <option value="gist_ncar">gist_ncar</option> | |
122 <option value="gist_rainbow">gist_rainbow</option> | |
123 <option value="gist_stern">gist_stern</option> | |
124 <option value="gist_yarg">gist_yarg</option> | |
125 <option value="gray">gray</option> | |
126 <option value="hot">hot</option> | |
127 <option value="hsv">hsv</option> | |
128 <option value="jet">jet</option> | |
129 <option value="pink">pink</option> | |
130 <option value="prism">prism</option> | |
131 <option value="spectral">spectral</option> | |
132 <option value="spring">spring</option> | |
133 <option value="summer">summer</option> | |
134 <option value="winter">winter</option> | |
135 </param> | |
136 </when> | |
137 </conditional> | |
138 </inputs> | |
139 | |
140 <outputs> | |
141 <expand macro="output_pipeline_macro" /> | |
142 </outputs> | |
143 | |
144 <tests> | |
145 <test> | |
146 <expand macro="test_input_pipeline_param" /> | |
147 <param name="input_object" value="Nuclei" /> | |
148 <param name="name_output_image" value="MaskNuclei" /> | |
149 <conditional name="con_color_format"> | |
150 <param name="color_format" value="Binary (black & white)" /> | |
151 </conditional> | |
152 <expand macro="test_out_file" file="convert_objects_to_image.txt" /> | |
153 </test> | |
154 </tests> | |
155 <expand macro="help" module="ConvertObjectsToImage" /> | |
156 <expand macro="citations" /> | |
157 </tool> |