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comparison rrparser.xml @ 7:de7b4c226b02 draft

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planemo upload for repository https://github.com/brsynth/rrparser commit a57357b9a0a5a7f5a4ac0e6fe3d00233afd11327
author tduigou
date Mon, 17 Mar 2025 14:56:07 +0000
parents ada9a9847d10
children d72f31975a06
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6:77845de246f9 7:de7b4c226b02
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@">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>
26 #if str($compress) == "true": 26 #if str($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($input_conditional_ec.input_type) == "in"
33 --ec '$input_conditional_ec.input_ec_in'
34 #end if
35 #if str($input_conditional_ec.input_type) == "out"
36 --ecx '$input_conditional_ec.input_ec_out'
31 #end if 37 #end if
32 ]]></command> 38 ]]></command>
33 <inputs> 39 <inputs>
34 <conditional name="rules"> 40 <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"> 41 <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">
58 <option selected="true" value="12">12</option> 64 <option selected="true" value="12">12</option>
59 <option selected="true" value="14">14</option> 65 <option selected="true" value="14">14</option>
60 <option selected="true" value="16">16</option> 66 <option selected="true" value="16">16</option>
61 </param> 67 </param>
62 <param name="compress" type="boolean" checked="false" label="Compress output" /> 68 <param name="compress" type="boolean" checked="false" label="Compress output" />
69 <conditional name="input_conditional_ec">
70 <param name="input_type" type="select" label="Filter based on EC number">
71 <option value="no" selected="True">No</option>
72 <option value="in">EC numbers to keep</option>
73 <option value="out">EC numbers to remove</option>
74 </param>
75 <when value="no" />
76 <when value="in">
77 <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
78 </when>
79 <when value="out">
80 <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
81 </when>
82 </conditional>
63 </inputs> 83 </inputs>
64 <outputs> 84 <outputs>
65 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" > 85 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
66 <change_format> 86 <change_format>
67 <when input="compress" format="tar" value="true"/> 87 <when input="compress" format="tar" value="true"/>
84 <param name="type" value="rules-file"/> 104 <param name="type" value="rules-file"/>
85 <param name="file" value="rules_in.csv" /> 105 <param name="file" value="rules_in.csv" />
86 </conditional> 106 </conditional>
87 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/> 107 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
88 </test> 108 </test>
109 <test>
110 <!-- test 4 -->
111 <conditional name="rules">
112 <param name="type" value="rules-file"/>
113 <param name="file" value="rules_in.csv" />
114 </conditional>
115 <conditional name="input_conditional_ec">
116 <param name="input_type" value="in"/>
117 <param name="input_ec_in" value="ec.csv"/>
118 </conditional>
119 <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
120 </test>
121 <test>
122 <!-- test 5 -->
123 <conditional name="rules">
124 <param name="type" value="rules-file"/>
125 <param name="file" value="rules_in.csv" />
126 </conditional>
127 <conditional name="input_conditional_ec">
128 <param name="input_type" value="out"/>
129 <param name="input_ec_out" value="ec.csv"/>
130 </conditional>
131 <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
132 </test>
133
89 </tests> 134 </tests>
90 <help><![CDATA[ 135 <help><![CDATA[
91 RRulesParser 136 RRulesParser
92 ============ 137 ============
93 138
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). 139 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).
95 140
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. 141 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.
97 142
98 Input 143 Input
99 ----- 144 -----
100 145
101 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file 146 * **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. 147 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
103 * **input_format**: (string) input file format (csv: default, tsv) 148 * **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 149 * **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
150 * **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.
105 151
106 Ouput 152 Ouput
107 ----- 153 -----
108 154
109 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes. 155 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.