Mercurial > repos > yating-l > gonramp_apollo_tools

annotate apolloUserManager.xml @ 2:4be6fcac4bf2 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
author yating-l
date Wed, 29 Nov 2017 15:39:32 -0500
parents 78af01d73add
children
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1 <tool id="apollo_user_manager" name="Apollo User Manager" version="1.0.0">
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2 <description>
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3 This Galaxy tool is used to manage Apollo users.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="3.0.3">apollo_api</requirement>
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11 </requirements>
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13 <stdio>
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14 </stdio>
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16 <command detect_errors="exit_code"><![CDATA[
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17 mkdir -p $output.extra_files_path;
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18 ## Dump the tool parameters into a JSON file
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19 python $json_file parameters.json;
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20 python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output
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21 ]]></command>
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22 <configfiles>
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23 <configfile name="json_file">
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24 import json
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25 import sys
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26
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27 file_path = sys.argv[1]
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28 #set global data_parameter_dict = {"operations": dict()}
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29 ## Function to retrieve the data of the inputs
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30 #def prepare_json($operation_type, $data_dict, $batch)
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31 #silent $data_dict.update({"batch": str($batch)})
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32 #if $operation_type in $data_parameter_dict["operations"]
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33 #silent $data_parameter_dict["operations"][$operation_type].append($data_dict)
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34 #else
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35 #set array_inputs = []
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36 #silent $array_inputs.append($data_dict)
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37 #silent $data_parameter_dict["operations"].update({$operation_type: $array_inputs})
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38 #end if
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39 #end def
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43
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44 #for $i, $f in enumerate($operation)
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45 #if $f.operation_type_selector.operation_type == "create"
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46 #set batch = $f.operation_type_selector.batch_selector.batch
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47 #if $batch == "false"
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48 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
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49 "firstname": str($f.operation_type_selector.batch_selector.firstname),
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50 "lastname": str($f.operation_type_selector.batch_selector.lastname),
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51 "password": str($f.operation_type_selector.batch_selector.password)}
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52
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53 #else
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54 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
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55 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
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56 #end if
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57 #silent $prepare_json("create", $data_dict, $batch)
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58
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59 #elif $f.operation_type_selector.operation_type == "delete"
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60 #set batch = $f.operation_type_selector.batch_selector.batch
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61 #if $batch == "false"
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62 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email)}
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63 #else
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64 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
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65 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
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66 #end if
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67 #silent $prepare_json("delete", $data_dict, $batch)
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68 #elif $f.operation_type_selector.operation_type == "add"
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69 #set batch = $f.operation_type_selector.batch_selector.batch
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70 #if $batch == "false"
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71 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
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72 "group": str($f.operation_type_selector.batch_selector.group_name)}
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73 #else
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74 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
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75 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
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76 #end if
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77 #silent $prepare_json("add", $data_dict, $batch)
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78 #elif $f.operation_type_selector.operation_type == "remove"
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79 #set batch = $f.operation_type_selector.batch_selector.batch
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80 #if $batch == "false"
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81 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
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82 "group": str($f.operation_type_selector.batch_selector.group_name)}
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83 #else
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84 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
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85 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
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86 #end if
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87 #silent $prepare_json("remove", $data_dict, $batch)
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88 #end if
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89 #end for
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90
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91
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92 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
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93 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
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94 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
1
78af01d73add planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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95 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
0
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96 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
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97 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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98 with open(file_path, 'w') as f:
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99 json.dump($data_parameter_dict, f)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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100 </configfile>
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101 </configfiles>
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102
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103
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104 <inputs>
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105 <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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106 <sanitizer>
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107 <valid initial="string.letters,string.digits">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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108 <add value="@-=_.()/+*^,:?!"/>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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109 </valid>
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110 </sanitizer>
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111 </param>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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112
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113 <param
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114 name="admin_password"
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115 type="text"
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116 label="Admin password"
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117 />
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118
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119 <repeat name="operation" title="New operation">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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120 <conditional name="operation_type_selector" >
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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121 <param name="operation_type" type="select" label="Create a user, delete a user, add a user to a group or remove a user from a group">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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122 <option value="create">Create a user</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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123 <option value="delete">Delete a users</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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124 <option value="add">Add a user to a group</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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125 <option value="remove">Remove a user from a group</option>
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126 </param>
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127 <when value="create">
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128 <conditional name="batch_selector">
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129 <param name="batch" type="select" label="Manipulate a single user or multiple users">
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130 <option value="false" selected="true">Single user</option>
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131 <option value="true">Multiple users</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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132 </param>
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133 <when value="false">
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134 <param name="user_email" type="text" label="User email" help="Specify the user email">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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135 <sanitizer>
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136 <valid initial="string.letters,string.digits">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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137 <add value="@-=_.()/+*^,:?!"/>
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138 </valid>
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139 </sanitizer>
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140 </param>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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141 <param name="firstname" type="text" label="First name" />
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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142 <param name="lastname" type="text" label="Last name" />
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143 <param name="password" type="text" label="Password" />
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144 </when>
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145 <when value="true">
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146 <expand macro="upload_text_file" />
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147 </when>
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148 </conditional>
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149 </when>
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150 <when value="delete">
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151 <conditional name="batch_selector">
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152 <param name="batch" type="select" label="Manipulate a single user or multiple users">
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153 <option value="false" selected="true">Single user</option>
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154 <option value="true">Multiple users</option>
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155 </param>
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156 <when value="false">
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157 <param name="user_email" type="text" label="User email" help="Specify the user email">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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158 <sanitizer>
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159 <valid initial="string.letters,string.digits">
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160 <add value="@-=_.()/+*^,:?!"/>
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161 </valid>
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162 </sanitizer>
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163 </param>
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164 </when>
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165 <when value="true">
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166 <expand macro="upload_text_file" />
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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167 </when>
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168 </conditional>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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169 </when>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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170 <when value="add">
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171 <conditional name="batch_selector">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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172 <param name="batch" type="select" label="Manipulate a single user or multiple users">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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173 <option value="false" selected="true">Single user</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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174 <option value="true">Multiple users</option>
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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175 </param>
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176 <when value="false">
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177 <param name="user_email" type="text" label="User email" help="Specify the user email">
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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178 <sanitizer>
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179 <valid initial="string.letters,string.digits">
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180 <add value="@-=_.()/+*^,:?!"/>
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181 </valid>
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182 </sanitizer>
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183 </param>
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184 <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
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185 </when>
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186 <when value="true">
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187 <expand macro="upload_text_file" />
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188 </when>
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189 </conditional>
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190 </when>
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191 <when value="remove">
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192 <conditional name="batch_selector">
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193 <param name="batch" type="select" label="Manipulate a single user or multiple users">
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194 <option value="false" selected="true">Single user</option>
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195 <option value="true">Multiple users</option>
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196 </param>
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197 <when value="false">
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198 <param name="user_email" type="text" label="User email" help="Specify the user email">
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199 <sanitizer>
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200 <valid initial="string.letters,string.digits">
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201 <add value="@-=_.()/+*^,:?!"/>
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202 </valid>
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203 </sanitizer>
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204 </param>
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205 <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
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206 </when>
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207 <when value="true">
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208 <expand macro="upload_text_file" />
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209 </when>
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210 </conditional>
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211 </when>
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212 </conditional>
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213 </repeat>
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214
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215 <conditional name="advanced_options">
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216 <param name="advanced_options_selector" type="select" label="Advanced options">
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217 <option value="off" selected="true">Hide advanced options</option>
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218 <option value="on">Display advanced options</option>
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219 </param>
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220 <!-- TODO: Avoid redundancy here -->
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221 <when value="on">
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222 <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
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223 <param name="debug_mode" type="select" label="Activate debug mode">
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224 <option value="false" selected="true">No</option>
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225 <option value="true">Yes</option>
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226 <help>
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227 Use this option if you are a G-OnRamp developer
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228 </help>
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229 </param>
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230 </when>
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231 <when value="off">
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232 <param name="port" type="hidden" value="8080" />
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233 <param name="debug_mode" type="hidden"
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234 value="false">
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235 </param>
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236 </when>
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237 </conditional>
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238 </inputs>
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239 <outputs>
1
78af01d73add planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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240 <data format="txt" name="output" label="${tool.name} on ${on_string}" />
0
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241 </outputs>
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242
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243 <help>
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244 This Galaxy tool is used to manage Apollo users.The currently supported operation including:
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245
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246 - Create a new user
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247 - Delete a user
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248 - Add a user to a group (If the group doesn't exist, create the group)
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249 - Remove a user to a group
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250
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251 The tool can do these operations on one student at a time. It can also do the operations on multiple students at a time by uploading a text file, which including students information.
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252
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253 The text file can be either CSV (comma-delimited) or Tabular (tab-delimited). It should have a header line, including names for each column. Example text files:
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254
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255 Text file for creating multiple users:
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256
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257 .. csv-table::
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258 :header: "useremail", "firstname", "lastname", "password"
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259 :widths: 20, 10, 10, 10
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260
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261 "test1@demo.com", "test1", "demo", "1234"
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262 "test2@demo.com", "test2", "demo", "1234"
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263 "test3@demo.com", "test3", "demo", "1234"
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264
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265
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266 Text file for deleting multiple users:
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267
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268 .. csv-table::
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269 :header: "useremail"
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270 :widths: 20
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271
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272 "test1@demo.com"
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273 "test2@demo.com"
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274 "test3@demo.com"
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275
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276
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277 Text file for adding / removing multiple users from a group:
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278
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279 .. csv-table::
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280 :header: "useremail", "group"
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281 :widths: 20, 20
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282
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283 "test1@demo.com", "annotation_group1"
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284 "test2@demo.com", "annotation_group1"
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285 "test3@demo.com", "annotation_group1"
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286
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287 </help>
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288 <citations>
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289 </citations>
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290 </tool>