Mercurial > repos > bgruening > cp_relate_objects

comparison relate_objects.xml @ 0:3a2cfcd7c38a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 17:44:27 -0400
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children b6f13e783ac5
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-1:000000000000 0:3a2cfcd7c38a
1 <tool id="cp_relate_objects" name="RelateObjects" version="@CP_VERSION@">
2 <description>assigns relationships parent-children between objects</description>
3 <macros>
4 <import>macros.xml</import>
5 <xml name="distToOtherParents">
6 <conditional name="con_other_parent_dist">
7 <param name="calc_dist_to_others" label="Calculate distances to other parents?" display="radio" type="select">
8 <option value="Yes">Yes</option>
9 <option value="No">No</option>
10 </param>
11 <when value="Yes">
12 <repeat name="rpt_parent_name" title="Parent Name">
13 <param name="other_parent_name" type="text" label="Parent name">
14 <expand macro="text_validator" />
15 </param>
16 </repeat>
17 </when>
18 <when value="No" />
19 </conditional>
20 </xml>
21 </macros>
22
23 <expand macro="py_requirements"/>
24 <expand macro="cmd_modules" />
25
26 <configfiles>
27 <inputs name="inputs" />
28 <configfile name="script_file">
29 import json
30 import sys
31 import os
32
33 FOURSPACES=@SPACES@
34
35 input_json_path = sys.argv[1]
36 input_pipeline= sys.argv[2]
37
38 params = json.load(open(input_json_path, "r"))
39
40 def writero():
41 _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
42
43 _str += FOURSPACES + "Parent objects:%s\n" % params['parent_objects']
44
45 _str += FOURSPACES + "Child objects:%s\n" % params['child_objects']
46 _str += FOURSPACES + "Calculate child-parent distances?:%s\n" % params['con_dist']['calc_dist']
47 _str += FOURSPACES + "Calculate per-parent means for all child measurements?:%s\n" % params['means_for_all']
48
49 dist_others = params['con_dist']['con_other_parent_dist']['calc_dist_to_others']
50
51 _str += FOURSPACES + "Calculate distances to other parents?:%s\n" % dist_others
52
53 name_flag = params['con_save_child']['save_child_as_new']
54 _str += FOURSPACES + "Do you want to save the children with parents as a new object set?:%s\n" % name_flag
55
56 if name_flag == "Yes":
57 _str += FOURSPACES + "Name the output object:%s\n" % params['con_save_child']['name_output']
58 else:
59 _str += FOURSPACES + "Name the output object:None\n"
60
61 if dist_others == "Yes":
62 for pname in params['con_dist']['con_other_parent_dist']['rpt_parent_name']:
63 _str += FOURSPACES + "Parent name:%s\n" % pname['other_parent_name']
64
65 return _str
66
67 with open(input_pipeline) as fin:
68 lines = fin.readlines()
69
70 k, v = lines[4].strip().split(':')
71
72 module_count = int(v)
73 new_count = module_count + 1
74 lines[4] = k + ":%d\n" % new_count
75 with open("output", "w") as f:
76 f.writelines(lines)
77 f.write(writero())
78
79 f.close()
80 </configfile>
81 </configfiles>
82
83 <inputs>
84 <expand macro="input_pipeline_macro"/>
85 <param name="parent_objects" label="Parent objects" type="text">
86 <expand macro="text_validator" />
87 </param>
88 <param name="child_objects" label="Child objects" type="text" >
89 <expand macro="text_validator" />
90 </param>
91 <param name="means_for_all" label="Calculate per-parent means for all child measurements?:" display="radio" type="select">
92 <option value="Yes">Yes</option>
93 <option value="No">No</option>
94 </param>
95 <conditional name="con_dist">
96 <param name="calc_dist" label="Calculate child-parent distances?" type="select">
97 <option value="None">None</option>
98 <option value="Centroid">Centroid</option>
99 <option value="Minimum">Minimum</option>
100 <option value="Both">Both</option>
101 </param>
102 <when value="Centroid">
103 <expand macro="distToOtherParents" />
104 </when>
105 <when value="Minimum">
106 <expand macro="distToOtherParents" />
107 </when>
108 <when value="Both">
109 <expand macro="distToOtherParents" />
110 </when>
111 <when value="None" />
112 </conditional>
113 <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">
115 <option value="Yes">Yes</option>
116 <option value="No">No</option>
117 </param>
118 <when value="Yes">
119 <param name="name_output" type="text" label="Name the output object">
120 <expand macro="text_validator" />
121 </param>
122 </when>
123 <when value="No" />
124 </conditional>
125 </inputs>
126
127 <outputs>
128 <expand macro="output_pipeline_macro" />
129 </outputs>
130
131 <tests>
132 <test>
133 <expand macro="test_input_pipeline_param" />
134
135 <param name="parent_objects" value="Nuclei" />
136 <param name="child_objects" value="Nucleoli" />
137 <param name="means_for_all" value="Yes" />
138 <conditional name="con_dist">
139 <param name="calc_dist" value="Both" />
140 <conditional name="con_other_parent_dist">
141 <param name="calc_dist_to_others" value="No" />
142 </conditional>
143 </conditional>
144 <conditional name="con_save_child">
145 <param name="save_child_as_new" value="Yes" />
146 <param name="name_output" value="RelateObjects" />
147 </conditional>
148
149 <expand macro="test_out_file" file="relate_objects.txt" />
150 </test>
151 </tests>
152
153 <expand macro="help" module="RelateObjects" />
154 <expand macro="citations" />
155
156 </tool>