Mercurial > repos > bgruening > cp_relate_objects

annotate relate_objects.xml @ 5:841ef3852f64 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:03:23 +0000
parents da52d2b10f59
children
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5
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1 <tool id="cp_relate_objects" name="RelateObjects" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
2
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2 <description>assign relationships parent-children between objects</description>
0
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3 <macros>
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4 <import>macros.xml</import>
5
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5 <token name="@VERSION_SUFFIX@">0</token>
0
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6 <xml name="distToOtherParents">
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7 <conditional name="con_other_parent_dist">
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8 <param name="calc_dist_to_others" label="Calculate distances to other parents?" display="radio" type="select">
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9 <option value="Yes">Yes</option>
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10 <option value="No">No</option>
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11 </param>
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12 <when value="Yes">
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13 <repeat name="rpt_parent_name" title="Parent Name">
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14 <param name="other_parent_name" type="text" label="Parent name">
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15 <expand macro="text_validator" />
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16 </param>
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17 </repeat>
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18 </when>
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19 <when value="No" />
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20 </conditional>
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21 </xml>
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22 </macros>
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23
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24 <expand macro="py_requirements"/>
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25 <expand macro="cmd_modules" />
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26
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27 <configfiles>
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28 <inputs name="inputs" />
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29 <configfile name="script_file">
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30 import json
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31 import sys
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32 import os
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33
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34 FOURSPACES=@SPACES@
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35
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36 input_json_path = sys.argv[1]
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37 input_pipeline= sys.argv[2]
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38
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39 params = json.load(open(input_json_path, "r"))
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40
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41 def writero():
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42 _str = "\nRelateObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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43
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44 _str += FOURSPACES + "Parent objects:%s\n" % params['parent_objects']
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45
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46 _str += FOURSPACES + "Child objects:%s\n" % params['child_objects']
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47 _str += FOURSPACES + "Calculate child-parent distances?:%s\n" % params['con_dist']['calc_dist']
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48 _str += FOURSPACES + "Calculate per-parent means for all child measurements?:%s\n" % params['means_for_all']
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49
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50 dist_others = params['con_dist']['con_other_parent_dist']['calc_dist_to_others']
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51
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52 _str += FOURSPACES + "Calculate distances to other parents?:%s\n" % dist_others
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53
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54 name_flag = params['con_save_child']['save_child_as_new']
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55 _str += FOURSPACES + "Do you want to save the children with parents as a new object set?:%s\n" % name_flag
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56
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57 if name_flag == "Yes":
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58 _str += FOURSPACES + "Name the output object:%s\n" % params['con_save_child']['name_output']
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59 else:
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60 _str += FOURSPACES + "Name the output object:None\n"
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61
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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62 if dist_others == "Yes":
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63 for pname in params['con_dist']['con_other_parent_dist']['rpt_parent_name']:
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64 _str += FOURSPACES + "Parent name:%s\n" % pname['other_parent_name']
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65
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66 return _str
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67
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68 with open(input_pipeline) as fin:
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69 lines = fin.readlines()
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70
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71 k, v = lines[4].strip().split(':')
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72
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73 module_count = int(v)
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74 new_count = module_count + 1
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75 lines[4] = k + ":%d\n" % new_count
3
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76 with open("output.cppipe", "w") as f:
0
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77 f.writelines(lines)
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78 f.write(writero())
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79
3
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80 f.close()
0
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81 </configfile>
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82 </configfiles>
3
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83
0
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84 <inputs>
3
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85 <expand macro="input_pipeline_param"/>
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86 <param name="parent_objects" label="Parent objects" value="Do not use" type="text" help="Parent objects are defined as those objects which encompass the child object. For example, when relating speckles to the nuclei that contain them, the nuclei are the parents.">
0
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87 <expand macro="text_validator" />
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88 </param>
3
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89 <param name="child_objects" label="Child objects" value="Do not use" type="text" help="Child objects are defined as those objects contained within the parent object. For example, when relating speckles to the nuclei that contains them, the speckles are the children.">
0
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90 <expand macro="text_validator" />
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91 </param>
3
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92 <param name="means_for_all" label="Calculate per-parent means for all child measurements?" display="radio" type="select">
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93 <help>
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94 <![CDATA[
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95 Select 'Yes' to calculate the per-parent mean values of every upstream measurement made with the children objects and store them as a measurement for the parent. This module must be placed after all the measure modules that make measurements of the children objects.
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96
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97 ]]>
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98 </help>
0
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99 <option value="Yes">Yes</option>
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100 <option value="No">No</option>
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101 </param>
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102 <conditional name="con_dist">
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103 <param name="calc_dist" label="Calculate child-parent distances?" type="select">
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104 <help>
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105 <![CDATA[
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106 Choose the method to calculate distances of each child to its parent.
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107 For example, these measurements can tell you whether nuclear speckles are located more closely to the center of the nucleus or to the nuclear periphery.
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108 <br> - None: Do not calculate any distances. This saves computation time.
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109 <br> - Minimum: The distance from the centroid of the child object to the closest perimeter point on the parent object.
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110 <br> - Centroid: The distance from the centroid of the child object to the centroid of the parent.
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111 <br> - Both: Calculate both the Minimum and Centroid distances.
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112 ]]>
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113 </help>
0
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114 <option value="None">None</option>
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115 <option value="Centroid">Centroid</option>
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116 <option value="Minimum">Minimum</option>
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117 <option value="Both">Both</option>
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118 </param>
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119 <when value="Centroid">
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120 <expand macro="distToOtherParents" />
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121 </when>
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122 <when value="Minimum">
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123 <expand macro="distToOtherParents" />
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124 </when>
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125 <when value="Both">
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126 <expand macro="distToOtherParents" />
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127 </when>
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128 <when value="None" />
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129 </conditional>
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130 <conditional name="con_save_child">
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131 <param name="save_child_as_new" label="Do you want to save the children with parents as a new object set?" display="radio" type="select" help="Select 'Yes' to save the children objects that do have parents as new object set. Objects with no parents will be discarded.">
0
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132 <option value="Yes">Yes</option>
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133 <option value="No">No</option>
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134 </param>
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135 <when value="Yes">
3
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136 <param name="name_output" type="text" value="RelateObjects" label="Enter a name for the output object">
0
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137 <expand macro="text_validator" />
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138 </param>
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139 </when>
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140 <when value="No" />
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141 </conditional>
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142 </inputs>
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143
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144 <outputs>
3
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145 <expand macro="output_pipeline_param" />
0
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146 </outputs>
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147
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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148 <tests>
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149 <test>
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150 <expand macro="test_input_pipeline_param" />
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151
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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152 <param name="parent_objects" value="Nuclei" />
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153 <param name="child_objects" value="Nucleoli" />
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154 <param name="means_for_all" value="Yes" />
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155 <conditional name="con_dist">
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156 <param name="calc_dist" value="Both" />
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157 <conditional name="con_other_parent_dist">
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158 <param name="calc_dist_to_others" value="No" />
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159 </conditional>
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160 </conditional>
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161 <conditional name="con_save_child">
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162 <param name="save_child_as_new" value="Yes" />
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163 <param name="name_output" value="RelateObjects" />
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164 </conditional>
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165
3
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166 <expand macro="test_out_file" file="relate_objects.cppipe" />
0
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167 </test>
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168 </tests>
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169
3
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170 <help>
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171 <![CDATA[
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172
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173 .. class:: infomark
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174
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175 **What it does**
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176
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177 RelateObjects assigns relationships; all objects (e.g., speckles) within a parent object (e.g., nucleus) become its children.
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178 This module allows you to associate child objects with parent objects.
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179 This is useful for counting the number of children associated with each parent, and for calculating mean measurement values for all children that are associated with each parent.
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180 An object will be considered a child even if the edge is the only partly touching a parent object.
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181 If a child object is touching multiple parent objects, the object will be assigned to the parent with maximal overlap.
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182 For an alternate approach to assigning parent/child relationships, consider using the MaskObjects module.
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183 If you want to include child objects that lie outside but still near parent objects, you might want to expand the parent objects using ExpandOrShrink or IdentifySecondaryObjects.
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184
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185 @COMMON_HELP@
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186 ]]>
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187 </help>
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188
0
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189 <expand macro="citations" />
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190
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191 </tool>