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annotate 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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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
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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@">1</token>
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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 '$adv.diameters'
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24 --output-format csv
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25 --rules-dir "\${TMPDIR:-.}"
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26 #if str($adv.compress) == "true":
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27 --outfile '$out_rules'.csv.gz
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28 && mv '$out_rules'.csv.gz '$out_rules'
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29 #else:
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30 --outfile '$out_rules'
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31 #end if
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32 #if str($adv.input_conditional_ec.input_type) == "in"
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33 --ec '$adv.input_conditional_ec.input_ec_in'
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34 #end if
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35 #if str($adv.input_conditional_ec.input_type) == "out"
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36 --ecx '$adv.input_conditional_ec.input_ec_out'
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37 #end if
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38 #if $adv.input_scores_file
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39 --scores '$adv.input_scores_file'
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40 #end if
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41 ]]></command>
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42 <inputs>
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43 <conditional name="rules">
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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">
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45 <option value="retro" selected="True">RetroRules (retro)</option>
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46 <option value="forward">RetroRules (forward)</option>
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47 <option value="all">RetroRules (all)</option>
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48 <option value="rules-file">Other reaction rules...</option>
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49 </param>
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50 <when value="retro"/>
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51 <when value="forward"/>
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52 <when value="all"/>
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53 <when value="rules-file">
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54 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
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55 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
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56 <option value="csv" selected="True">csv</option>
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57 <option value="tsv">tsv</option>
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58 </param>
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59 </when>
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60 </conditional>
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61 <section name="adv" title="Advanced Options" expanded="false" >
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62 <param name="compress" type="boolean" checked="false" label="Compress output" />
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63 <param name="input_scores_file" type="data" format="csv" optional="True" label="Score File" help="Filename containing rules names and scores" />
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64 <conditional name="input_conditional_ec">
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65 <param name="input_type" type="select" label="Filter based on EC number">
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66 <option value="no" selected="True">No</option>
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67 <option value="in">EC numbers to keep</option>
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68 <option value="out">EC numbers to remove</option>
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69 </param>
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70 <when value="no" />
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71 <when value="in">
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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" />
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73 </when>
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74 <when value="out">
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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" />
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76 </when>
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77 </conditional>
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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">
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79 <option selected="true" value="2">2</option>
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80 <option selected="true" value="4">4</option>
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81 <option selected="true" value="6">6</option>
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82 <option selected="true" value="8">8</option>
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83 <option selected="true" value="10">10</option>
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84 <option selected="true" value="12">12</option>
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85 <option selected="true" value="14">14</option>
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86 <option selected="true" value="16">16</option>
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87 </param>
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88 </section>
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89
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90 </inputs>
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91 <outputs>
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92 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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93 <change_format>
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94 <when input="compress" format="tar" value="true"/>
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95 </change_format>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <!-- test 1: check if identical outputs are produced with default parameters-->
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101 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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102 </test>
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103 <test>
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104 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
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105 <section name="adv">
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106 <param name="diameters" value="2,4,6"/>
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107 </section>
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108 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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109 </test>
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110 <test>
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111 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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112 <conditional name="rules">
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113 <param name="type" value="rules-file"/>
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114 <param name="file" value="rules_in.csv" />
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115 </conditional>
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116 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
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117 </test>
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118 <test>
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119 <!-- test 4 -->
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120 <conditional name="rules">
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121 <param name="type" value="rules-file"/>
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122 <param name="file" value="rules_in.csv" />
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123 </conditional>
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124 <section name="adv">
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125 <conditional name="input_conditional_ec">
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126 <param name="input_type" value="in"/>
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127 <param name="input_ec_in" value="ec.csv"/>
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128 </conditional>
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129 </section>
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130 <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
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131 </test>
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132 <test>
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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 -->
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134 <conditional name="rules">
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135 <param name="type" value="rules-file"/>
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136 <param name="file" value="rules_in.csv" />
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137 </conditional>
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138 <section name="adv">
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139 <conditional name="input_conditional_ec">
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140 <param name="input_type" value="out"/>
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141 <param name="input_ec_out" value="ec.csv"/>
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142 </conditional>
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143 </section>
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144 <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
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145 </test>
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146 <test>
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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 -->
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148 <conditional name="rules">
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149 <param name="type" value="rules-file"/>
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150 <param name="file" value="rules_in.csv" />
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151 </conditional>
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152 <section name="adv" >
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153 <param name="input_scores_file" value="scores.csv" />
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154 </section>
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155 <output name="out_rules" file="rules_scores.csv" ftype="csv" compare="diff"/>
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156 </test>
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157 </tests>
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158 <help><![CDATA[
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159 RRulesParser
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160 ============
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161
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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).
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163
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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.
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165
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166 Input
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167 -----
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168
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169 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
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170 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
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171 * **input_format**: (string) input file format (csv: default, tsv)
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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
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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.
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174 * **Scores file**: file containing rules names and scores
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175
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176 Ouput
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177 -----
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178
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179 * **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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180 ]]></help>
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181 <creator>
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182 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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183 </creator>
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184 <citations>
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185 <citation type="doi">10.1093/nar/gky940</citation>
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186 </citations>
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187 </tool>