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comparison rrparser.xml @ 4:3f39c7d3c14e draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Tue, 21 Jun 2022 14:39:03 +0000
parents 392f18980ff4
children d7882cf07d98
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3:392f18980ff4 4:3f39c7d3c14e
1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@" profile="19.09"> 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="@TOOL_VERSION@">2.4.6</token> 5 <token name="@TOOL_VERSION@">2.4.6</token>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
8 </requirements> 9 </requirements>
10 <regex match="WARNING:" level="warning" /> 11 <regex match="WARNING:" level="warning" />
11 <regex match="ERROR:" level="fatal" /> 12 <regex match="ERROR:" level="fatal" />
12 </stdio> 13 </stdio>
13 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
14 python -m rrparser 15 python -m rrparser
15 #if str($rules.type) != "other": 16 #if str($rules.type) != "rules-file":
16 retrorules 17 retrorules
17 --rule-type '$rules.type' 18 --rule-type '$rules.type'
18 #else: 19 #else:
19 '$rules.file' 20 '$rules.file'
20 --input-format '$rules.format' 21 --input-format '$rules.input_format'
21 #end if 22 #end if
22 --diameters '$diameters' 23 --diameters '$diameters'
23 --output-format csv 24 --output-format csv
24 #if str($compress) == "true": 25 #if str($compress) == "true":
25 --outfile '$out_rules'.csv.gz 26 --outfile '$out_rules'.csv.gz
28 --outfile '$out_rules' 29 --outfile '$out_rules'
29 #end if 30 #end if
30 ]]></command> 31 ]]></command>
31 <inputs> 32 <inputs>
32 <conditional name="rules"> 33 <conditional name="rules">
33 <param name="type" type="select" label="Rule Type" help=""> 34 <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">
34 <option value="retro" selected="True">RetroRules (retro)</option> 35 <option value="retro" selected="True">RetroRules (retro)</option>
35 <option value="forward">RetroRules (forward)</option> 36 <option value="forward">RetroRules (forward)</option>
36 <option value="all">RetroRules (all)</option> 37 <option value="all">RetroRules (all)</option>
37 <option value="other">Other reaction rules...</option> 38 <option value="rules-file">Other reaction rules...</option>
38 </param> 39 </param>
39 <when value="other"> 40 <when value="rules-file">
40 <param name="file" type="data" format="csv" optional="False" label="Rules File"/> 41 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
41 <param name="format" type="select" optional="False" label="File format"> 42 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
42 <option value="csv" selected="True">csv</option> 43 <option value="csv" selected="True">csv</option>
43 <option value="tsv">tsv</option> 44 <option value="tsv">tsv</option>
44 </param> 45 </param>
45 </when> 46 </when>
46 </conditional> 47 </conditional>
47 <param name="diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules"> 48 <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">
48 <option selected="true" value="2">2</option> 49 <option selected="true" value="2">2</option>
49 <option selected="true" value="4">4</option> 50 <option selected="true" value="4">4</option>
50 <option selected="true" value="6">6</option> 51 <option selected="true" value="6">6</option>
51 <option selected="true" value="8">8</option> 52 <option selected="true" value="8">8</option>
52 <option selected="true" value="10">10</option> 53 <option selected="true" value="10">10</option>
53 <option selected="true" value="12">12</option> 54 <option selected="true" value="12">12</option>
54 <option selected="true" value="14">14</option> 55 <option selected="true" value="14">14</option>
55 <option selected="true" value="16">16</option> 56 <option selected="true" value="16">16</option>
56 </param> 57 </param>
57 <param name="compress" type="boolean" display="checkboxes" label="Compress output" /> 58 <param name="compress" type="boolean" checked="false" label="Compress output" />
58 </inputs> 59 </inputs>
59 <outputs> 60 <outputs>
60 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" > 61 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
61 <change_format> 62 <change_format>
62 <when input="compress" format="tar" value="true"/> 63 <when input="compress" format="tar" value="true"/>
74 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/> 75 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
75 </test> 76 </test>
76 <test> 77 <test>
77 <!-- test 3: check if identical outputs are produced with csv input rules file--> 78 <!-- test 3: check if identical outputs are produced with csv input rules file-->
78 <conditional name="rules"> 79 <conditional name="rules">
79 <param name="type" value="other"/> 80 <param name="type" value="rules-file"/>
80 <param name="file" value="rules_in.csv" /> 81 <param name="file" value="rules_in.csv" />
81 </conditional> 82 </conditional>
82 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/> 83 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
83 </test> 84 </test>
84 </tests> 85 </tests>
85 <help><![CDATA[ 86 <help><![CDATA[
86 RRulesParser 87 RRulesParser
87 ============ 88 ============
88 89
89 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_ 90 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).
91
92 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.
90 93
91 Input 94 Input
92 ----- 95 -----
93 96
94 * **rules-file**: (string) Filename of reaction rules 97 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
95 * **input-format**: (string) input file format (default: csv) 98 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
96 * **rule-type**: (string) {all,retro,forward} rule usage to filter from rules file 99 * **input_format**: (string) input file format (csv: default, tsv)
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 100 * **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)
99 101
100 Ouput 102 Ouput
101 ----- 103 -----
102 104
103 * **outfile**: (string): file where results are written. If file ends with '.gz', it will be gzipped. 105 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
104
105 106
106 Version 107 Version
107 ------- 108 -------
108 109
109 v2.4.6 110 v2.4.6