Mercurial > repos > bgruening > cp_relate_objects

annotate relate_objects.xml @ 6:48102a685037 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 09:27:30 +0000
parents 3a3033222f61
children
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3a3033222f61 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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1 <tool id="cp_relate_objects" name="RelateObjects" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
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48102a685037 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with CellProfiler</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">1</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 <edam_operations>
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25 <edam_operation>operation_3443</edam_operation>
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26 </edam_operations>
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27 <xrefs>
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28 <xref type="bio.tools">CellProfiler</xref>
48102a685037 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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29 <xref type="biii">cellprofiler</xref>
48102a685037 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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30 </xrefs>
48102a685037 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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31
0
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32 <expand macro="py_requirements"/>
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 <expand macro="cmd_modules" />
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35 <configfiles>
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36 <inputs name="inputs" />
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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37 <configfile name="script_file">
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38 import json
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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39 import sys
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40 import os
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42 FOURSPACES=@SPACES@
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44 input_json_path = sys.argv[1]
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45 input_pipeline= sys.argv[2]
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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46
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47 params = json.load(open(input_json_path, "r"))
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48
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49 def writero():
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50 _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
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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51
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52 _str += FOURSPACES + "Parent objects:%s\n" % params['parent_objects']
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53
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54 _str += FOURSPACES + "Child objects:%s\n" % params['child_objects']
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55 _str += FOURSPACES + "Calculate child-parent distances?:%s\n" % params['con_dist']['calc_dist']
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56 _str += FOURSPACES + "Calculate per-parent means for all child measurements?:%s\n" % params['means_for_all']
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57
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58 dist_others = params['con_dist']['con_other_parent_dist']['calc_dist_to_others']
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59
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60 _str += FOURSPACES + "Calculate distances to other parents?:%s\n" % dist_others
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61
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62 name_flag = params['con_save_child']['save_child_as_new']
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63 _str += FOURSPACES + "Do you want to save the children with parents as a new object set?:%s\n" % name_flag
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64
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65 if name_flag == "Yes":
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66 _str += FOURSPACES + "Name the output object:%s\n" % params['con_save_child']['name_output']
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67 else:
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68 _str += FOURSPACES + "Name the output object:None\n"
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69
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70 if dist_others == "Yes":
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71 for pname in params['con_dist']['con_other_parent_dist']['rpt_parent_name']:
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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72 _str += FOURSPACES + "Parent name:%s\n" % pname['other_parent_name']
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74 return _str
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76 with open(input_pipeline) as fin:
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77 lines = fin.readlines()
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78
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79 k, v = lines[4].strip().split(':')
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80
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81 module_count = int(v)
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82 new_count = module_count + 1
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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83 lines[4] = k + ":%d\n" % new_count
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84 with open("output.cppipe", "w") as f:
0
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85 f.writelines(lines)
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86 f.write(writero())
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87
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88 f.close()
0
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89 </configfile>
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90 </configfiles>
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91
0
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92 <inputs>
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93 <expand macro="input_pipeline_param"/>
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94 <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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95 <expand macro="text_validator" />
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96 </param>
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97 <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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98 <expand macro="text_validator" />
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99 </param>
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100 <param name="means_for_all" label="Calculate per-parent means for all child measurements?" display="radio" type="select">
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101 <help>
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102 <![CDATA[
f3f45c42bc36 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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103 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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104
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105 ]]>
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106 </help>
0
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107 <option value="Yes">Yes</option>
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108 <option value="No">No</option>
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109 </param>
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110 <conditional name="con_dist">
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111 <param name="calc_dist" label="Calculate child-parent distances?" type="select">
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112 <help>
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113 <![CDATA[
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114 Choose the method to calculate distances of each child to its parent.
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115 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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116 <br> - None: Do not calculate any distances. This saves computation time.
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117 <br> - Minimum: The distance from the centroid of the child object to the closest perimeter point on the parent object.
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118 <br> - Centroid: The distance from the centroid of the child object to the centroid of the parent.
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119 <br> - Both: Calculate both the Minimum and Centroid distances.
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120 ]]>
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121 </help>
0
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122 <option value="None">None</option>
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123 <option value="Centroid">Centroid</option>
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124 <option value="Minimum">Minimum</option>
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125 <option value="Both">Both</option>
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126 </param>
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127 <when value="Centroid">
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128 <expand macro="distToOtherParents" />
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129 </when>
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130 <when value="Minimum">
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131 <expand macro="distToOtherParents" />
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132 </when>
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133 <when value="Both">
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134 <expand macro="distToOtherParents" />
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135 </when>
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136 <when value="None" />
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137 </conditional>
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138 <conditional name="con_save_child">
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139 <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
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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140 <option value="Yes">Yes</option>
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141 <option value="No">No</option>
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142 </param>
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143 <when value="Yes">
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144 <param name="name_output" type="text" value="RelateObjects" label="Enter a name for the output object">
0
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145 <expand macro="text_validator" />
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146 </param>
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147 </when>
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148 <when value="No" />
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149 </conditional>
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150 </inputs>
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151
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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152 <outputs>
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153 <expand macro="output_pipeline_param" />
0
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154 </outputs>
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155
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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156 <tests>
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157 <test>
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158 <expand macro="test_input_pipeline_param" />
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159
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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160 <param name="parent_objects" value="Nuclei" />
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161 <param name="child_objects" value="Nucleoli" />
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162 <param name="means_for_all" value="Yes" />
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163 <conditional name="con_dist">
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164 <param name="calc_dist" value="Both" />
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165 <conditional name="con_other_parent_dist">
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166 <param name="calc_dist_to_others" value="No" />
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167 </conditional>
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168 </conditional>
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169 <conditional name="con_save_child">
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170 <param name="save_child_as_new" value="Yes" />
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171 <param name="name_output" value="RelateObjects" />
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172 </conditional>
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173
3
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174 <expand macro="test_out_file" file="relate_objects.cppipe" />
0
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175 </test>
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176 </tests>
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177
3
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178 <help>
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179 <![CDATA[
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180
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181 .. class:: infomark
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182
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183 **What it does**
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184
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185 RelateObjects assigns relationships; all objects (e.g., speckles) within a parent object (e.g., nucleus) become its children.
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186 This module allows you to associate child objects with parent objects.
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187 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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188 An object will be considered a child even if the edge is the only partly touching a parent object.
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189 If a child object is touching multiple parent objects, the object will be assigned to the parent with maximal overlap.
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190 For an alternate approach to assigning parent/child relationships, consider using the MaskObjects module.
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191 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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192
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193 @COMMON_HELP@
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194 ]]>
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195 </help>
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196
0
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197 <expand macro="citations" />
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198
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199 </tool>