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comparison rrparser.xml @ 2:8d1e0ca750aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 83279dc554c34566720f3857ac914a2e4fd85a8d
author iuc
date Thu, 20 Mar 2025 07:23:56 +0000
parents 46d4ac243530
children 39198f1ee8e8
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1:46d4ac243530 2:8d1e0ca750aa
1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Retrieve the reaction rules from RetroRules</description> 2 <description>Retrieve the reaction rules from RetroRules</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">2.5.2</token> 5 <token name="@TOOL_VERSION@">2.6.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
36 <option value="retro" selected="True">RetroRules (retro)</option> 36 <option value="retro" selected="True">RetroRules (retro)</option>
37 <option value="forward">RetroRules (forward)</option> 37 <option value="forward">RetroRules (forward)</option>
38 <option value="all">RetroRules (all)</option> 38 <option value="all">RetroRules (all)</option>
39 <option value="rules-file">Other reaction rules...</option> 39 <option value="rules-file">Other reaction rules...</option>
40 </param> 40 </param>
41 <when value="retro"/>
42 <when value="forward"/>
43 <when value="all"/>
41 <when value="rules-file"> 44 <when value="rules-file">
42 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/> 45 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
43 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)"> 46 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
44 <option value="csv" selected="True">csv</option> 47 <option value="csv" selected="True">csv</option>
45 <option value="tsv">tsv</option> 48 <option value="tsv">tsv</option>
88 RRulesParser 91 RRulesParser
89 ============ 92 ============
90 93
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). 94 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).
92 95
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. 96 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) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
94 97
95 Input 98 Input
96 ----- 99 -----
97 100
98 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file 101 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
106 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes. 109 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
107 110
108 Version 111 Version
109 ------- 112 -------
110 113
111 v2.5.0 114 v2.6.0
112 115
113 Authors 116 Authors
114 ------- 117 -------
115 118
116 * **Thomas Duigou** 119 * **Thomas Duigou**