Mercurial > repos > bgruening > cp_relate_objects

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