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annotate rrparser.xml @ 1:7ee6e2bc2936 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit f8407d9bdd216bcc12ea1bda3177112ae28235c4
author iuc
date Thu, 13 Apr 2023 07:26:47 +0000
parents 0a6e076541f6
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0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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2 <description>Retrieve the reaction rules from RetroRules</description>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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7ee6e2bc2936 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit f8407d9bdd216bcc12ea1bda3177112ae28235c4
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5 <token name="@TOOL_VERSION@">2.5.2</token>
0
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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6 </macros>
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7 <requirements>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
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9 </requirements>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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10 <stdio>
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11 <regex match="WARNING:" level="warning" />
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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12 <regex match="ERROR:" level="fatal" />
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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13 </stdio>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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14 <command detect_errors="exit_code"><![CDATA[
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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15 python -m rrparser
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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16 #if str($rules.type) != "rules-file":
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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17 --rules_file retrorules
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18 --rule-type '$rules.type'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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19 #else:
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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20 --rules_file '$rules.file'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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21 --input-format '$rules.input_format'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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22 #end if
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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23 --diameters '$diameters'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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24 --output-format csv
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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25 --rules-dir "\${TMPDIR:-.}"
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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26 #if str($compress) == "true":
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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27 --outfile '$out_rules'.csv.gz
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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28 && mv '$out_rules'.csv.gz '$out_rules'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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29 #else:
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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30 --outfile '$out_rules'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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31 #end if
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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32 ]]></command>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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33 <inputs>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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34 <conditional name="rules">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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35 <param name="type" type="select" label="Rule Type" help="Return the rules that are in reverse, forward, both direction or from an input user file">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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36 <option value="retro" selected="True">RetroRules (retro)</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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37 <option value="forward">RetroRules (forward)</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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38 <option value="all">RetroRules (all)</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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39 <option value="rules-file">Other reaction rules...</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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40 </param>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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41 <when value="rules-file">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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42 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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43 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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44 <option value="csv" selected="True">csv</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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45 <option value="tsv">tsv</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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46 </param>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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47 </when>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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48 </conditional>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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49 <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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50 <option selected="true" value="2">2</option>
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51 <option selected="true" value="4">4</option>
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52 <option selected="true" value="6">6</option>
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53 <option selected="true" value="8">8</option>
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54 <option selected="true" value="10">10</option>
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55 <option selected="true" value="12">12</option>
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56 <option selected="true" value="14">14</option>
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57 <option selected="true" value="16">16</option>
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58 </param>
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59 <param name="compress" type="boolean" checked="false" label="Compress output" />
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60 </inputs>
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61 <outputs>
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62 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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63 <change_format>
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64 <when input="compress" format="tar" value="true"/>
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65 </change_format>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <!-- test 1: check if identical outputs are produced with default parameters-->
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71 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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72 </test>
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73 <test>
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74 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
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75 <param name="diameters" value="2,4,6"/>
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76 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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77 </test>
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78 <test>
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79 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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80 <conditional name="rules">
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81 <param name="type" value="rules-file"/>
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82 <param name="file" value="rules_in.csv" />
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83 </conditional>
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84 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88 RRulesParser
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89 ============
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90
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91 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_ extracted from public databases and expressed in the community-standard SMARTS (SMILES arbitrary target specification) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center).
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92
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93 The generated output is a file containing reaction rules which are generic descriptions of chemical reactions that can be used in retrosynthesis workflows (e.g. `Retrosynthesis KNIME Workflow <https://www.myexperiment.org/workflows/4987/versions/2.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
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94
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95 Input
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96 -----
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97
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98 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
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99 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
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100 * **input_format**: (string) input file format (csv: default, tsv)
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101 * **diameters**: (integer list) diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules
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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 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
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107
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108 Version
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109 -------
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110
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111 v2.5.0
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112
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113 Authors
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114 -------
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115
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116 * **Thomas Duigou**
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117 * Melchior du Lac
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118 * Joan Hérisson
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119
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120 License
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121 -------
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122
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123 This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
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124
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125 Acknowledgments
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126 ---------------
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127
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128 * Joan Hérisson
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129
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130 ]]></help>
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131 <citations>
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132 <citation type="doi">10.1093/nar/gky940 </citation>
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133 </citations>
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134 </tool>