Mercurial > repos > bgruening > cp_relate_objects

comparison relate_objects.xml @ 3:f3f45c42bc36 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:53:35 -0400
parents b6f13e783ac5
children 3a3033222f61
comparison
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2:b6f13e783ac5 3:f3f45c42bc36
70 k, v = lines[4].strip().split(':') 70 k, v = lines[4].strip().split(':')
71 71
72 module_count = int(v) 72 module_count = int(v)
73 new_count = module_count + 1 73 new_count = module_count + 1
74 lines[4] = k + ":%d\n" % new_count 74 lines[4] = k + ":%d\n" % new_count
75 with open("output", "w") as f: 75 with open("output.cppipe", "w") as f:
76 f.writelines(lines) 76 f.writelines(lines)
77 f.write(writero()) 77 f.write(writero())
78 78
79 f.close() 79 f.close()
80 </configfile> 80 </configfile>
81 </configfiles> 81 </configfiles>
82 82
83 <inputs> 83 <inputs>
84 <expand macro="input_pipeline_macro"/> 84 <expand macro="input_pipeline_param"/>
85 <param name="parent_objects" label="Parent objects" type="text"> 85 <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.">
86 <expand macro="text_validator" /> 86 <expand macro="text_validator" />
87 </param> 87 </param>
88 <param name="child_objects" label="Child objects" type="text" > 88 <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.">
89 <expand macro="text_validator" /> 89 <expand macro="text_validator" />
90 </param> 90 </param>
91 <param name="means_for_all" label="Calculate per-parent means for all child measurements?:" display="radio" type="select"> 91 <param name="means_for_all" label="Calculate per-parent means for all child measurements?" display="radio" type="select">
92 <help>
93 <![CDATA[
94 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.
95
96 ]]>
97 </help>
92 <option value="Yes">Yes</option> 98 <option value="Yes">Yes</option>
93 <option value="No">No</option> 99 <option value="No">No</option>
94 </param> 100 </param>
95 <conditional name="con_dist"> 101 <conditional name="con_dist">
96 <param name="calc_dist" label="Calculate child-parent distances?" type="select"> 102 <param name="calc_dist" label="Calculate child-parent distances?" type="select">
103 <help>
104 <![CDATA[
105 Choose the method to calculate distances of each child to its parent.
106 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.
107 <br> - None: Do not calculate any distances. This saves computation time.
108 <br> - Minimum: The distance from the centroid of the child object to the closest perimeter point on the parent object.
109 <br> - Centroid: The distance from the centroid of the child object to the centroid of the parent.
110 <br> - Both: Calculate both the Minimum and Centroid distances.
111 ]]>
112 </help>
97 <option value="None">None</option> 113 <option value="None">None</option>
98 <option value="Centroid">Centroid</option> 114 <option value="Centroid">Centroid</option>
99 <option value="Minimum">Minimum</option> 115 <option value="Minimum">Minimum</option>
100 <option value="Both">Both</option> 116 <option value="Both">Both</option>
101 </param> 117 </param>
109 <expand macro="distToOtherParents" /> 125 <expand macro="distToOtherParents" />
110 </when> 126 </when>
111 <when value="None" /> 127 <when value="None" />
112 </conditional> 128 </conditional>
113 <conditional name="con_save_child"> 129 <conditional name="con_save_child">
114 <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"> 130 <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.">
115 <option value="Yes">Yes</option> 131 <option value="Yes">Yes</option>
116 <option value="No">No</option> 132 <option value="No">No</option>
117 </param> 133 </param>
118 <when value="Yes"> 134 <when value="Yes">
119 <param name="name_output" type="text" label="Name the output object"> 135 <param name="name_output" type="text" value="RelateObjects" label="Enter a name for the output object">
120 <expand macro="text_validator" /> 136 <expand macro="text_validator" />
121 </param> 137 </param>
122 </when> 138 </when>
123 <when value="No" /> 139 <when value="No" />
124 </conditional> 140 </conditional>
125 </inputs> 141 </inputs>
126 142
127 <outputs> 143 <outputs>
128 <expand macro="output_pipeline_macro" /> 144 <expand macro="output_pipeline_param" />
129 </outputs> 145 </outputs>
130 146
131 <tests> 147 <tests>
132 <test> 148 <test>
133 <expand macro="test_input_pipeline_param" /> 149 <expand macro="test_input_pipeline_param" />
144 <conditional name="con_save_child"> 160 <conditional name="con_save_child">
145 <param name="save_child_as_new" value="Yes" /> 161 <param name="save_child_as_new" value="Yes" />
146 <param name="name_output" value="RelateObjects" /> 162 <param name="name_output" value="RelateObjects" />
147 </conditional> 163 </conditional>
148 164
149 <expand macro="test_out_file" file="relate_objects.txt" /> 165 <expand macro="test_out_file" file="relate_objects.cppipe" />
150 </test> 166 </test>
151 </tests> 167 </tests>
152 168
153 <expand macro="help" module="RelateObjects" /> 169 <help>
170 <![CDATA[
171
172 .. class:: infomark
173
174 **What it does**
175
176 RelateObjects assigns relationships; all objects (e.g., speckles) within a parent object (e.g., nucleus) become its children.
177 This module allows you to associate child objects with parent objects.
178 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.
179 An object will be considered a child even if the edge is the only partly touching a parent object.
180 If a child object is touching multiple parent objects, the object will be assigned to the parent with maximal overlap.
181 For an alternate approach to assigning parent/child relationships, consider using the MaskObjects module.
182 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.
183
184 @COMMON_HELP@
185 ]]>
186 </help>
187
154 <expand macro="citations" /> 188 <expand macro="citations" />
155 189
156 </tool> 190 </tool>