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annotate mask_image.xml @ 6:667a513e67e4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:24:38 +0000
parents b178453ea8d1
children
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1 <tool id="cp_mask_image" name="MaskImage" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>with CellProfiler</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <token name="@VERSION_SUFFIX@">1</token>
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7 </macros>
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9 <edam_operations>
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10 <edam_operation>operation_3443</edam_operation>
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11 </edam_operations>
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12 <xrefs>
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13 <xref type="bio.tools">CellProfiler</xref>
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14 <xref type="biii">cellprofiler</xref>
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15 </xrefs>
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17 <expand macro="py_requirements"/>
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18 <expand macro="cmd_modules" />
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20 <configfiles>
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21 <inputs name="inputs"/>
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22 <configfile name="script_file">
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23 import json
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24 import sys
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25 import os
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27 FOURSPACES=@SPACES@
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29 input_json_path = sys.argv[1]
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30 input_pipeline= sys.argv[2]
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32 params = json.load(open(input_json_path, "r"))
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34 def writemi():
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35 _str = "\nMaskImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\'Keep only nucleoli inside the nuclei\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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37 _str += FOURSPACES + "Select the input image:%s\n" % params['input_image']
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38 _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']
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40 img_obj = params['con_img_obj']['img_obj']
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42 _str += FOURSPACES + "Use objects or an image as a mask?:%s\n" % params['con_img_obj']['img_obj']
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44 if img_obj == "Objects":
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45 _str += FOURSPACES + "Select object for mask:%s\n" % params['con_img_obj']['select_obj']
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46 _str += FOURSPACES + "Select image for mask:None\n"
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47 else:
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48 _str += FOURSPACES + "Select object for mask:None\n"
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49 _str += FOURSPACES + "Select image for mask:%s\n" % params['con_img_obj']['select_img']
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51 _str += FOURSPACES + "Invert the mask?:%s\n" % params['invert_mask']
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53 return _str
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55 with open(input_pipeline) as fin:
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56 lines = fin.readlines()
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58 k, v = lines[4].strip().split(':')
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60 module_count = int(v)
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61 new_count = module_count + 1
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62 lines[4] = k + ":%d\n" % new_count
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63
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64 with open("output.cppipe", "w") as f:
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65 f.writelines(lines)
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66 f.write(writemi())
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67
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68 f.close()
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69 </configfile>
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70 </configfiles>
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72 <inputs>
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74 <expand macro="input_pipeline_param" />
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75 <param name="input_image" label="Enter the name of the input image" type="text">
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76 <expand macro="text_validator" />
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77 </param>
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78
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79 <param name="name_output_image" type="text" label="Enter the name of the resulting image">
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80 <expand macro="text_validator" />
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81 </param>
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83 <conditional name="con_img_obj">
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84 <param name="img_obj" label="Use objects or an image as a mask?" type="select">
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85 <help>
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86 <![CDATA[
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87 You can mask an image in two ways:
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88 <br> - Objects: Using objects created by another module (for instance IdentifyPrimaryObjects).
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89 The module will mask out all parts of the image that are not within one of the objects (unless you invert the mask).
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90 <br> - Image: Using a binary image as the mask, where black portions of the image (false or zero-value pixels) will be masked out.
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91 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).
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92 You can use Threshold instead to create a binary image with finer control over the intensity choice.
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93 ]]>
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94 </help>
0
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95 <option value="Objects">Objects</option>
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96 <option value="Image">Image</option>
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97 </param>
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98 <when value="Objects">
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99 <param name="select_obj" label="Enter the name objects to mask the input image" type="text"/>
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100 </when>
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101 <when value="Image">
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102 <param name="select_img" label="Select image for mask" type="text"/>
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103 </when>
0
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104 </conditional>
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105 <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
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106 <help>
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107 <![CDATA[
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108 This option reverses the foreground/background relationship of the mask.
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109 <br> - Select "No" to produce the mask from the foreground (white portion) of the masking image or the area within the masking objects.
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110 <br> - Select "Yes" to instead produce the mask from the background (black portions) of the masking image or the area outside the masking objects.
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111 ]]>
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112 </help>
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113 <option value="Yes">Yes</option>
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114 <option value="No">No</option>
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115 </param>
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116 </inputs>
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117
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118 <outputs>
3
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119 <expand macro="output_pipeline_param" />
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120 </outputs>
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121
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122 <tests>
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123 <test>
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124 <expand macro="test_input_pipeline_param"/>
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125 <param name="input_image" value="DNAdarkholes" />
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126 <param name="name_output_image" value="MaskDNAdarkholes" />
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127 <conditional name="con_img_obj">
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128 <param name="img_obj" value="Objects" />
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129 <param name="select_obj" value="Nuclei" />
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130 </conditional>
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131 <param name="invert_mask" value="No" />
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132 <expand macro="test_out_file" file="mask_image.cppipe" />
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133 </test>
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134 </tests>
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135
3
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136 <help>
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137 <![CDATA[
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138 .. class:: infomark
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139
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140 **What it does**
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141
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142 This tool masks an image so you can use the mask downstream in the pipeline.
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143 The masked image is based on the original image and the masking object or image that is selected.
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144 If using a masking image, the mask is composed of the foreground (white portions);
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145 if using a masking object, the mask is composed of the area within the object.
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146 Note that the image created by this tool for further processing downstream is grayscale.
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147 If a binary mask is desired in subsequent tools, use the Threshold tool instead of MaskImage.
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148
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149 @COMMON_HELP@
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150 ]]>
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151 </help>
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152
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153 <expand macro="citations" />
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154
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155 </tool>