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comparison rrparser.xml @ 7:90e260b93a3a draft

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planemo upload for repository https://github.com/brsynth/rrparser commit b06816a566855a3f5c83b85fed0923853e562549-dirty
author tduigou
date Wed, 02 Apr 2025 08:16:50 +0000
parents d7882cf07d98
children 2ec2fae2a58d
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6:e40594345e48 7:90e260b93a3a
1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> 1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
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@">1</token>
5 <token name="@TOOL_VERSION@">2.5.2</token> 5 <token name="@TOOL_VERSION@">2.7.0</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>
18 --rule-type '$rules.type' 18 --rule-type '$rules.type'
19 #else: 19 #else:
20 --rules_file '$rules.file' 20 --rules_file '$rules.file'
21 --input-format '$rules.input_format' 21 --input-format '$rules.input_format'
22 #end if 22 #end if
23 --diameters '$diameters' 23 --diameters '$adv.diameters'
24 --output-format csv 24 --output-format csv
25 --rules-dir "\${TMPDIR:-.}" 25 --rules-dir "\${TMPDIR:-.}"
26 #if str($compress) == "true": 26 #if str($adv.compress) == "true":
27 --outfile '$out_rules'.csv.gz 27 --outfile '$out_rules'.csv.gz
28 && mv '$out_rules'.csv.gz '$out_rules' 28 && mv '$out_rules'.csv.gz '$out_rules'
29 #else: 29 #else:
30 --outfile '$out_rules' 30 --outfile '$out_rules'
31 #end if
32 #if str($adv.input_conditional_ec.input_type) == "in"
33 --ec '$adv.input_conditional_ec.input_ec_in'
34 #end if
35 #if str($adv.input_conditional_ec.input_type) == "out"
36 --ecx '$adv.input_conditional_ec.input_ec_out'
37 #end if
38 #if $adv.input_scores_file
39 --scores '$adv.input_scores_file'
31 #end if 40 #end if
32 ]]></command> 41 ]]></command>
33 <inputs> 42 <inputs>
34 <conditional name="rules"> 43 <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"> 44 <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">
47 <option value="csv" selected="True">csv</option> 56 <option value="csv" selected="True">csv</option>
48 <option value="tsv">tsv</option> 57 <option value="tsv">tsv</option>
49 </param> 58 </param>
50 </when> 59 </when>
51 </conditional> 60 </conditional>
52 <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"> 61 <section name="adv" title="Advanced Options" expanded="false" >
53 <option selected="true" value="2">2</option> 62 <param name="compress" type="boolean" checked="false" label="Compress output" />
54 <option selected="true" value="4">4</option> 63 <param name="input_scores_file" type="data" format="csv" optional="True" label="Score File" help="Filename containing rules names and scores" />
55 <option selected="true" value="6">6</option> 64 <conditional name="input_conditional_ec">
56 <option selected="true" value="8">8</option> 65 <param name="input_type" type="select" label="Filter based on EC number">
57 <option selected="true" value="10">10</option> 66 <option value="no" selected="True">No</option>
58 <option selected="true" value="12">12</option> 67 <option value="in">EC numbers to keep</option>
59 <option selected="true" value="14">14</option> 68 <option value="out">EC numbers to remove</option>
60 <option selected="true" value="16">16</option> 69 </param>
61 </param> 70 <when value="no" />
62 <param name="compress" type="boolean" checked="false" label="Compress output" /> 71 <when value="in">
72 <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
73 </when>
74 <when value="out">
75 <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
76 </when>
77 </conditional>
78 <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">
79 <option selected="true" value="2">2</option>
80 <option selected="true" value="4">4</option>
81 <option selected="true" value="6">6</option>
82 <option selected="true" value="8">8</option>
83 <option selected="true" value="10">10</option>
84 <option selected="true" value="12">12</option>
85 <option selected="true" value="14">14</option>
86 <option selected="true" value="16">16</option>
87 </param>
88 </section>
89
63 </inputs> 90 </inputs>
64 <outputs> 91 <outputs>
65 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" > 92 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
66 <change_format> 93 <change_format>
67 <when input="compress" format="tar" value="true"/> 94 <when input="compress" format="tar" value="true"/>
73 <!-- test 1: check if identical outputs are produced with default parameters--> 100 <!-- test 1: check if identical outputs are produced with default parameters-->
74 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/> 101 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
75 </test> 102 </test>
76 <test> 103 <test>
77 <!-- test 2: check if identical outputs are produced with diameters=2,4,6--> 104 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
78 <param name="diameters" value="2,4,6"/> 105 <section name="adv">
106 <param name="diameters" value="2,4,6"/>
107 </section>
79 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/> 108 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
80 </test> 109 </test>
81 <test> 110 <test>
82 <!-- test 3: check if identical outputs are produced with csv input rules file--> 111 <!-- test 3: check if identical outputs are produced with csv input rules file-->
83 <conditional name="rules"> 112 <conditional name="rules">
84 <param name="type" value="rules-file"/> 113 <param name="type" value="rules-file"/>
85 <param name="file" value="rules_in.csv" /> 114 <param name="file" value="rules_in.csv" />
86 </conditional> 115 </conditional>
87 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/> 116 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
88 </test> 117 </test>
118 <test>
119 <!-- test 4 -->
120 <conditional name="rules">
121 <param name="type" value="rules-file"/>
122 <param name="file" value="rules_in.csv" />
123 </conditional>
124 <section name="adv">
125 <conditional name="input_conditional_ec">
126 <param name="input_type" value="in"/>
127 <param name="input_ec_in" value="ec.csv"/>
128 </conditional>
129 </section>
130 <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
131 </test>
132 <test>
133 <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
134 <conditional name="rules">
135 <param name="type" value="rules-file"/>
136 <param name="file" value="rules_in.csv" />
137 </conditional>
138 <section name="adv">
139 <conditional name="input_conditional_ec">
140 <param name="input_type" value="out"/>
141 <param name="input_ec_out" value="ec.csv"/>
142 </conditional>
143 </section>
144 <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
145 </test>
146 <test>
147 <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile rules_scores.csv -scores scores.csv -->
148 <conditional name="rules">
149 <param name="type" value="rules-file"/>
150 <param name="file" value="rules_in.csv" />
151 </conditional>
152 <section name="adv" >
153 <param name="input_scores_file" value="scores.csv" />
154 </section>
155 <output name="out_rules" file="rules_scores.csv" ftype="csv" compare="diff"/>
156 </test>
89 </tests> 157 </tests>
90 <help><![CDATA[ 158 <help><![CDATA[
91 RRulesParser 159 RRulesParser
92 ============ 160 ============
93 161
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). 162 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).
95 163
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 <https://www.myexperiment.org/workflows/4987/versions/2.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. 164 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.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
97 165
98 Input 166 Input
99 ----- 167 -----
100 168
101 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file 169 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
102 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format. 170 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
103 * **input_format**: (string) input file format (csv: default, tsv) 171 * **input_format**: (string) input file format (csv: default, tsv)
104 * **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 172 * **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
173 * **EC numbers to filter**: retain or remove some EC numbers. A file is expected containing EC numbers separated by a comma on the first line.
174 * **Scores file**: file containing rules names and scores
105 175
106 Ouput 176 Ouput
107 ----- 177 -----
108 178
109 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes. 179 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.