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comparison rrparser.xml @ 1:ea590c609fec draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 02 Feb 2022 14:29:14 +0000
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0:024dcd6421db 1:ea590c609fec
1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@" profile="19.09">
2 <description>Retrieve the reaction rules from RetroRules</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.4.6</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
8 </requirements>
9 <stdio>
10 <regex match="WARNING:" level="warning" />
11 <regex match="ERROR:" level="fatal" />
12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[
14 python -m rrparser
15 #if str($rules.type) != "other":
16 retrorules
17 --rule-type '$rules.type'
18 #else:
19 '$rules.file'
20 --input-format '$rules.format'
21 #end if
22 --diameters '$diameters'
23 --output-format csv
24 #if str($compress) == "true":
25 --outfile '$out_rules'.csv.gz
26 && mv '$out_rules'.csv.gz '$out_rules'
27 #else:
28 --outfile '$out_rules'
29 #end if
30 ]]></command>
31 <inputs>
32 <conditional name="rules">
33 <param name="type" type="select" label="Rule Type" help="">
34 <option value="retro" selected="True">RetroRules (retro)</option>
35 <option value="forward">RetroRules (forward)</option>
36 <option value="all">RetroRules (all)</option>
37 <option value="other">Other reaction rules...</option>
38 </param>
39 <when value="other">
40 <param name="file" type="data" format="csv" optional="False" label="Rules File"/>
41 <param name="format" type="select" optional="False" label="File format">
42 <option value="csv" selected="True">csv</option>
43 <option value="tsv">tsv</option>
44 </param>
45 </when>
46 </conditional>
47 <param name="diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules">
48 <option selected="true" value="2">2</option>
49 <option selected="true" value="4">4</option>
50 <option selected="true" value="6">6</option>
51 <option selected="true" value="8">8</option>
52 <option selected="true" value="10">10</option>
53 <option selected="true" value="12">12</option>
54 <option selected="true" value="14">14</option>
55 <option selected="true" value="16">16</option>
56 </param>
57 <param name="compress" type="boolean" display="checkboxes" label="Compress output" />
58 </inputs>
59 <outputs>
60 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
61 <change_format>
62 <when input="compress" format="tar" value="true"/>
63 </change_format>
64 </data>
65 </outputs>
66 <tests>
67 <test>
68 <!-- test 1: check if identical outputs are produced with default parameters-->
69 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
70 </test>
71 <test>
72 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
73 <param name="diameters" value="2,4,6"/>
74 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
75 </test>
76 <test>
77 <!-- test 3: check if identical outputs are produced with csv input rules file-->
78 <conditional name="rules">
79 <param name="type" value="other"/>
80 <param name="file" value="rules_in.csv" />
81 </conditional>
82 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
83 </test>
84 </tests>
85 <help><![CDATA[
86 RRulesParser
87 ============
88
89 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_
90
91 Input
92 -----
93
94 * **rules-file**: (string) Filename of reaction rules
95 * **input-format**: (string) input file format (default: csv)
96 * **rule-type**: (string) {all,retro,forward} rule usage to filter from rules file
97 * **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
98 * **output-format**: (string) {csv,tsv} output file format (default: csv)
99
100 Ouput
101 -----
102
103 * **outfile**: (string): file where results are written. If file ends with '.gz', it will be gzipped.
104
105
106 Version
107 -------
108
109 v2.4.6
110
111 Authors
112 -------
113
114 * **Thomas Duigou**
115 * Melchior du Lac
116 * Joan Hérisson
117
118 License
119 -------
120
121 This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
122
123 Acknowledgments
124 ---------------
125
126 * Joan Hérisson
127
128 ]]></help>
129 <citations>
130 <citation type="doi">10.1093/nar/gky940 </citation>
131 </citations>
132 </tool>