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annotate rrparser.xml @ 3:39198f1ee8e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 2a3d0848e53a4030a54eff826521ccca6da45985
author iuc
date Mon, 07 Apr 2025 07:57:05 +0000
parents 8d1e0ca750aa
children 74a2f8fd3306
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19fb8488cdbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Retrieve the reaction rules from RetroRules</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
3
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5 <token name="@TOOL_VERSION@">2.7.0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="WARNING:" level="warning" />
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12 <regex match="ERROR:" level="fatal" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python -m rrparser
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16 #if str($rules.type) != "rules-file":
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17 --rules_file retrorules
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18 --rule-type '$rules.type'
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19 #else:
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20 --rules_file '$rules.file'
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21 --input-format '$rules.input_format'
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22 #end if
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23 --diameters '$diameters'
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24 --output-format csv
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25 --rules-dir "\${TMPDIR:-.}"
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26 #if str($compress) == "true":
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27 --outfile '$out_rules'.csv.gz
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28 && mv '$out_rules'.csv.gz '$out_rules'
19fb8488cdbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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29 #else:
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30 --outfile '$out_rules'
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31 #end if
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32 ]]></command>
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33 <inputs>
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34 <conditional name="rules">
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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">
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36 <option value="retro" selected="True">RetroRules (retro)</option>
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37 <option value="forward">RetroRules (forward)</option>
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38 <option value="all">RetroRules (all)</option>
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39 <option value="rules-file">Other reaction rules...</option>
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40 </param>
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41 <when value="retro"/>
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42 <when value="forward"/>
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43 <when value="all"/>
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44 <when value="rules-file">
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45 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
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46 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
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47 <option value="csv" selected="True">csv</option>
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48 <option value="tsv">tsv</option>
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49 </param>
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50 </when>
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51 </conditional>
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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">
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53 <option selected="true" value="2">2</option>
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54 <option selected="true" value="4">4</option>
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55 <option selected="true" value="6">6</option>
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56 <option selected="true" value="8">8</option>
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57 <option selected="true" value="10">10</option>
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58 <option selected="true" value="12">12</option>
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59 <option selected="true" value="14">14</option>
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60 <option selected="true" value="16">16</option>
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61 </param>
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62 <param name="compress" type="boolean" checked="false" label="Compress output" />
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63 </inputs>
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64 <outputs>
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65 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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66 <change_format>
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67 <when input="compress" format="tar" value="true"/>
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68 </change_format>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <!-- test 1: check if identical outputs are produced with default parameters-->
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74 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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75 </test>
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76 <test>
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77 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
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78 <param name="diameters" value="2,4,6"/>
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79 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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80 </test>
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81 <test>
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82 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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83 <conditional name="rules">
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84 <param name="type" value="rules-file"/>
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85 <param name="file" value="rules_in.csv" />
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86 </conditional>
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87 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 RRulesParser
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92 ============
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93
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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).
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95
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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) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
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98 Input
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99 -----
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100
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101 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
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102 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
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103 * **input_format**: (string) input file format (csv: default, tsv)
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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
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105
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106 Ouput
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107 -----
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108
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109 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
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110
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111 Version
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112 -------
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113
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114 v2.6.0
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116 Authors
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117 -------
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118
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119 * **Thomas Duigou**
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120 * Melchior du Lac
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121 * Joan Hérisson
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122
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123 License
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124 -------
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125
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126 This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
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127
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128 Acknowledgments
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129 ---------------
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131 * Joan Hérisson
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133 ]]></help>
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134 <citations>
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135 <citation type="doi">10.1093/nar/gky940 </citation>
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136 </citations>
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137 </tool>