Mercurial > repos > bgruening > cp_mask_image

comparison mask_image.xml @ 3:ca1421f7e3ed draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:57:09 -0400
parents baa3e6d4d99d
children b178453ea8d1
comparison
equal deleted inserted replaced
2:baa3e6d4d99d 3:ca1421f7e3ed
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <expand macro="py_requirements"/> 8 <expand macro="py_requirements"/>
9 <expand macro="cmd_modules" /> 9 <expand macro="cmd_modules" />
10 10
11 <configfiles> 11 <configfiles>
12 <inputs name="inputs"/> 12 <inputs name="inputs"/>
13 <configfile name="script_file"> 13 <configfile name="script_file">
14 import json 14 import json
50 50
51 module_count = int(v) 51 module_count = int(v)
52 new_count = module_count + 1 52 new_count = module_count + 1
53 lines[4] = k + ":%d\n" % new_count 53 lines[4] = k + ":%d\n" % new_count
54 54
55 with open("output", "w") as f: 55 with open("output.cppipe", "w") as f:
56 f.writelines(lines) 56 f.writelines(lines)
57 f.write(writemi()) 57 f.write(writemi())
58 58
59 f.close() 59 f.close()
60 </configfile> 60 </configfile>
61 </configfiles> 61 </configfiles>
62 62
63 <inputs> 63 <inputs>
64 64
65 <expand macro="input_pipeline_macro" /> 65 <expand macro="input_pipeline_param" />
66 <param name="input_image" label="Select input image" type="text"> 66 <param name="input_image" label="Enter the name of the input image" type="text">
67 <expand macro="text_validator" /> 67 <expand macro="text_validator" />
68 </param> 68 </param>
69 69
70 <param name="name_output_image" type="text" label="Name the output image"> 70 <param name="name_output_image" type="text" label="Enter the name of the resulting image">
71 <expand macro="text_validator" /> 71 <expand macro="text_validator" />
72 </param> 72 </param>
73 73
74 <conditional name="con_img_obj"> 74 <conditional name="con_img_obj">
75 <param name="img_obj" label="Use objects or an image as a mask?" type="select"> 75 <param name="img_obj" label="Use objects or an image as a mask?" type="select">
76 <help>
77 <![CDATA[
78 You can mask an image in two ways:
79 <br> - Objects: Using objects created by another module (for instance IdentifyPrimaryObjects).
80 The module will mask out all parts of the image that are not within one of the objects (unless you invert the mask).
81 <br> - Image: Using a binary image as the mask, where black portions of the image (false or zero-value pixels) will be masked out.
82 If the image is not binary, the module will use all pixels whose intensity is greater than 0.5 as the mask’s foreground (white area).
83 You can use Threshold instead to create a binary image with finer control over the intensity choice.
84 ]]>
85 </help>
76 <option value="Objects">Objects</option> 86 <option value="Objects">Objects</option>
77 <option value="Image">Image</option> 87 <option value="Image">Image</option>
78 </param> 88 </param>
79 <when value="Objects"> 89 <when value="Objects">
80 <param name="select_obj" label="Select object for mask" type="text"/> 90 <param name="select_obj" label="Enter the name objects to mask the input image" type="text"/>
81 </when> 91 </when>
82 <when value="Image"> 92 <when value="Image">
83 <param name="select_img" label="Select image for mask" type="text"/> 93 <param name="select_img" label="Select image for mask" type="text"/>
84 </when> 94 </when>
85 </conditional> 95 </conditional>
86 <param name="invert_mask" label="Invert the mask?" type="select" display="radio"> 96 <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
97 <help>
98 <![CDATA[
99 This option reverses the foreground/background relationship of the mask.
100 <br> - Select "No" to produce the mask from the foreground (white portion) of the masking image or the area within the masking objects.
101 <br> - Select "Yes" to instead produce the mask from the background (black portions) of the masking image or the area outside the masking objects.
102 ]]>
103 </help>
87 <option value="Yes">Yes</option> 104 <option value="Yes">Yes</option>
88 <option value="No">No</option> 105 <option value="No">No</option>
89 </param> 106 </param>
90 </inputs> 107 </inputs>
91 108
92 <outputs> 109 <outputs>
93 <expand macro="output_pipeline_macro" /> 110 <expand macro="output_pipeline_param" />
94 </outputs> 111 </outputs>
95 112
96 <tests> 113 <tests>
97 <test> 114 <test>
98 <expand macro="test_input_pipeline_param"/> 115 <expand macro="test_input_pipeline_param"/>
101 <conditional name="con_img_obj"> 118 <conditional name="con_img_obj">
102 <param name="img_obj" value="Objects" /> 119 <param name="img_obj" value="Objects" />
103 <param name="select_obj" value="Nuclei" /> 120 <param name="select_obj" value="Nuclei" />
104 </conditional> 121 </conditional>
105 <param name="invert_mask" value="No" /> 122 <param name="invert_mask" value="No" />
106 <expand macro="test_out_file" file="mask_image.txt" /> 123 <expand macro="test_out_file" file="mask_image.cppipe" />
107 </test> 124 </test>
108 </tests> 125 </tests>
109 126
110 <expand macro="help" module="GrayToColor" /> 127 <help>
128 <![CDATA[
129 .. class:: infomark
130
131 **What it does**
132
133 This tool masks an image so you can use the mask downstream in the pipeline.
134 The masked image is based on the original image and the masking object or image that is selected.
135 If using a masking image, the mask is composed of the foreground (white portions);
136 if using a masking object, the mask is composed of the area within the object.
137 Note that the image created by this tool for further processing downstream is grayscale.
138 If a binary mask is desired in subsequent tools, use the Threshold tool instead of MaskImage.
139
140 @COMMON_HELP@
141 ]]>
142 </help>
143
111 <expand macro="citations" /> 144 <expand macro="citations" />
112 145
113 </tool> 146 </tool>