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annotate neo4jsbml.xml @ 1:0fa7de2ceeb7 draft

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planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
author tduigou
date Fri, 29 Sep 2023 11:15:40 +0000
parents 52fab09a8a36
children eea256ad4d7f
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52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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1 <tool id="neo4jsbml" name="Neo4jSbml" version="@TOOL_VERSION@" profile="21.09" license="MIT">
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2 <description>Import SBML file into Neo4j</description>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.11.1</token>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
1
0fa7de2ceeb7 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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10 python -m neo4jsbml
0
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11 --input-protocol-str '$input_protocol_str'
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12 --input-url-str '$input_url_str'
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13 --input-port-int '$input_port_int'
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14 --input-user-str '$input_user_str'
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15 --input-password-file '$input_password_file'
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16 --input-database-str '$input_database_str'
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17
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18 --input-file-sbml '$input_file_sbml'
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19 #if str($input_tag_str) != ""
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20 --input-tag-str '$input_tag_str'
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21 #end if
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22 --input-modelisation-json '$input_modelisation_json' > '$output_log'
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23 ]]></command>
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24 <inputs>
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25 <param name="input_protocol_str" type="select" label="Protocol">
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26 <option value="neo4j" selected="true">neo4j</option>
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27 <option value="neo4j+s">neo4j+s</option>
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28 <option value="neo4j+ssc">neo4j+ssc</option>
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29 <option value="bolt">bolt</option>
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30 <option value="bolt+s">bolt+s</option>
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31 <option value="bolt+ssc">bolt+ssc</option>
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32 </param>
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33 <param name="input_url_str" type="text" label="Url of the database">
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34 <validator type="empty_field" message="Not empty"/>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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35 </param>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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36 <param name="input_port_int" type="text" value="7687" label="Port of the database">
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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37 <validator type="empty_field" message="Not empty"/>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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38 <validator type="regex" message="Only integers are allowed">^(?:\d+)$</validator>
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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39 </param>
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40 <param name="input_user_str" type="text" value="neo4j" label="Username of the database">
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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41 <validator type="empty_field" message="Not empty"/>
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42 </param>
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43 <param name="input_password_file" type="data" format="txt" label="Password of the database"/>
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44 <param name="input_database_str" type="text" label="Database name">
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45 <validator type="empty_field" message="Not empty"/>
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46 </param>
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47
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48 <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
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49 <param name="input_tag_str" type="text" label="Identifier of the model"/>
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50 <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
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51 </inputs>
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52 <outputs>
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53 <data name="output_log" format="txt" label="${tool.name} - log" />
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54 </outputs>
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55 <help><![CDATA[
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56 Neo4jSbml
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57 =========
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58
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59 Step 1
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60 ------
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61
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62 Create a schema with [arrows](https://arrows.app), following these rules:
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63 .. image:: ${static_path}/images/PathwayModelisation-1.0.0.arrows.png
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64 :width: 90 %
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65 :align: center
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66
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67 Rules:
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68 * Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_
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69 * Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_
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70
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71 Step 2
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72 ------
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73 Export your schema at the JSON format.
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74 .. image:: ${static_path}/images/arrows.dwl.png
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75 :width: 90 %
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76 :align: center
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77
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78 Step 3
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79 ------
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80
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81 Import your data with `neo4jsbml` into Neo4j.
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82 * Use either a configuration file `ini` or individual parameters
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83 * Password needs to be store in a file for safety security
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84 * If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
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85
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86
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87 Inputs
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88 ------
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89
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90 Database parameters
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91 * **Protocol**: choose the protocol (default: neo4j)
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92 * **Url of the database**: define the url of the database
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93 * **Port of the database**: define the port of the database (default: 7687)
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94 * **Username of the database**: User name of the database
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95 * **Password of the database**: file with the password
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96 * **Database name**: database name
52fab09a8a36 planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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97
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98 Input
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99 * **SBML model**: SBML model
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100 * **Identifier of the model**: Associate an ID to the nodes
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101 * **Arrow's schema**: Schema created with Arrow
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102
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103 Ouput
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104 -----
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105
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106 * Traceback of the tool
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107 ]]></help>
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108 <citations>
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109 <citation type="bibtex">
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110 @unpublished{neo4jsbml
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111 author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon},
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112 title = {{Neo4jSbml}},
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113 url = {https://github.com/brsynth/neo4jsbml/},
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114 }
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115 </citation>
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116 </citations>
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117 </tool>