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comparison rrparser.xml @ 0:0a6e076541f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
author iuc
date Mon, 27 Jun 2022 20:27:06 +0000
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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>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">2.5.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
9 </requirements>
10 <stdio>
11 <regex match="WARNING:" level="warning" />
12 <regex match="ERROR:" level="fatal" />
13 </stdio>
14 <command detect_errors="exit_code"><![CDATA[
15 python -m rrparser
16 #if str($rules.type) != "rules-file":
17 --rules_file retrorules
18 --rule-type '$rules.type'
19 #else:
20 --rules_file '$rules.file'
21 --input-format '$rules.input_format'
22 #end if
23 --diameters '$diameters'
24 --output-format csv
25 --rules-dir "\${TMPDIR:-.}"
26 #if str($compress) == "true":
27 --outfile '$out_rules'.csv.gz
28 && mv '$out_rules'.csv.gz '$out_rules'
29 #else:
30 --outfile '$out_rules'
31 #end if
32 ]]></command>
33 <inputs>
34 <conditional name="rules">
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">
36 <option value="retro" selected="True">RetroRules (retro)</option>
37 <option value="forward">RetroRules (forward)</option>
38 <option value="all">RetroRules (all)</option>
39 <option value="rules-file">Other reaction rules...</option>
40 </param>
41 <when value="rules-file">
42 <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)">
44 <option value="csv" selected="True">csv</option>
45 <option value="tsv">tsv</option>
46 </param>
47 </when>
48 </conditional>
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">
50 <option selected="true" value="2">2</option>
51 <option selected="true" value="4">4</option>
52 <option selected="true" value="6">6</option>
53 <option selected="true" value="8">8</option>
54 <option selected="true" value="10">10</option>
55 <option selected="true" value="12">12</option>
56 <option selected="true" value="14">14</option>
57 <option selected="true" value="16">16</option>
58 </param>
59 <param name="compress" type="boolean" checked="false" label="Compress output" />
60 </inputs>
61 <outputs>
62 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
63 <change_format>
64 <when input="compress" format="tar" value="true"/>
65 </change_format>
66 </data>
67 </outputs>
68 <tests>
69 <test>
70 <!-- test 1: check if identical outputs are produced with default parameters-->
71 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
72 </test>
73 <test>
74 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
75 <param name="diameters" value="2,4,6"/>
76 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
77 </test>
78 <test>
79 <!-- test 3: check if identical outputs are produced with csv input rules file-->
80 <conditional name="rules">
81 <param name="type" value="rules-file"/>
82 <param name="file" value="rules_in.csv" />
83 </conditional>
84 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
85 </test>
86 </tests>
87 <help><![CDATA[
88 RRulesParser
89 ============
90
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).
92
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.
94
95 Input
96 -----
97
98 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
99 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
100 * **input_format**: (string) input file format (csv: default, tsv)
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
102
103 Ouput
104 -----
105
106 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
107
108 Version
109 -------
110
111 v2.5.0
112
113 Authors
114 -------
115
116 * **Thomas Duigou**
117 * Melchior du Lac
118 * Joan Hérisson
119
120 License
121 -------
122
123 This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
124
125 Acknowledgments
126 ---------------
127
128 * Joan Hérisson
129
130 ]]></help>
131 <citations>
132 <citation type="doi">10.1093/nar/gky940 </citation>
133 </citations>
134 </tool>