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annotate retrorules.xml @ 4:bd5ffc799c16 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
author tduigou
date Mon, 15 Sep 2025 12:57:08 +0000
parents cfa70e3fe1a4
children
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4
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1 <tool id="retrorules" name="RetroRules" version="1.0+galaxy2" profile="21.09" license="MIT">
0
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2 <description>Querying the RetroRules REST API</description>
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3 <requirements>
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4 <requirement type="package" version="2">requests</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/'query.py
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8 #if str($cond_src.from_src) == 'from_templates' or str($cond_src.from_src) == 'from_templates_count'
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9 #if str($cond_src.from_src) == 'from_templates'
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10 templates
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11 #elif str($cond_src.from_src) == 'from_templates_count'
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12 templates-count
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13 #end if
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14 --input-smarts-str '$cond_src.smarts'
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15 #set template_ids = []
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16 #for $x in $cond_src.rep_template_ids
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17 #silent template_ids.append(str($x.template_id))
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18 #end for
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19 #set template_id = ' '.join($template_ids)
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20 --input-template-ids-str $template_id
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21 #set reaction_ids = []
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22 #for $x in $cond_src.rep_reaction_ids
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23 #silent reaction_ids.append(str($x.reaction_id))
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24 #end for
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25 #set reaction_id = ' '.join($reaction_ids)
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26 --input-reaction-ids-str $reaction_id
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27 --input-datasets-str '$cond_src.from_datasets'
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28 --input-chemical-domain-str '$cond_src.from_chemical_domain'
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29 #if str($cond_src.ec_number) != ''
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30 --input-ec-number-str '$cond_src.ec_number'
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31 #end if
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32 #if str($cond_src.min_radius) != ''
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33 --input-min-radius-int '$cond_src.min_radius'
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34 #end if
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35 --input-valid-str '$cond_src.from_valid'
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36 #set dedup = 'false'
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37 #if str($cond_src.dedup) == 'true'
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38 #set dedup = 'true'
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39 #end if
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40 --input-dedup-str $dedup
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41 #if str($cond_src.from_src) == 'from_templates'
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42 #if str($cond_src.limit) != ''
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43 --input-limit-int '$cond_src.limit'
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44 #end if
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45 #if str($cond_src.offset) != ''
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46 --input-offset-int '$cond_src.offset'
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47 #end if
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48 #end if
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49 #elif str($cond_src.from_src) == 'from_templates_summary'
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50 templates-summary
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51 --input-template-id-str '$cond_src.template_id'
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52 #elif str($cond_src.from_src) == 'from_templates_sources'
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53 templates-sources
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54 --input-template-id-str '$cond_src.template_id'
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55 #end if
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56 --output-data-json '$output_json'
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57 ]]></command>
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58 <inputs>
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59 <conditional name="cond_src">
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60 <param name="from_src" type="select" multiple="False" label="Select entry point">
3
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61 <option value="from_templates" selected="True">Search templates</option>
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62 <option value="from_templates_summary">Summarize a template</option>
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63 <option value="from_templates_sources">List source reactions for a template</option>
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64 <option value="from_templates_count">Count templates</option>
0
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65 </param>
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66 <when value="from_templates">
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67 <param name="smarts" type="text" value="" label="Exact SMARTS">
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68 <sanitizer sanitize="false" />
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69 </param>
3
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70 <repeat name="rep_template_ids" title="Template">
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71 <param name="template_id" type="text" label="ID">
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72 <validator type="empty_field" message="Not empty" />
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73 </param>
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74 </repeat>
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75 <repeat name="rep_reaction_ids" title="Reaction">
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76 <param name="reaction_id" type="text" label="ID">
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77 <validator type="empty_field" message="Not empty" />
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78 </param>
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79 </repeat>
3
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80 <param name="from_datasets" type="select" multiple="False"
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81 label="Select a specific database">
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82 <option value="any" selected="True">Any</option>
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83 <option value="metanetx">MetaNetX</option>
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84 <option value="rhea">Rhea</option>
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85 <option value="uspto">USPTO</option>
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86 </param>
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87 <param name="from_chemical_domain" type="select" multiple="False"
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88 label="Chemical domain">
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89 <option value="any" selected="True">Any</option>
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90 <option value="biochem">Biochem</option>
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91 <option value="orgchem">Orgchem</option>
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92 </param>
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93 <param name="ec_number" type="text" value="" label="EC number to filter templates" />
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94 <param name="min_radius" type="integer" min="0" max="10" optional="True"
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95 label="Single radius filter" />
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96 <param name="from_valid" type="select" multiple="False" label="Filter by validity">
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97 <option value="true" selected="True">True</option>
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98 <option value="any">Any</option>
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99 <option value="false">False</option>
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100 </param>
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101 <param name="dedup" type="boolean" checked="True"
4
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102 label="By default deduplicated templates are returned" />
3
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103 <param name="limit" type="integer" min="1" optional="True"
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104 label="Limit number of returned templates" />
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105 <param name="offset" type="integer" min="0" optional="True"
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106 label="Offset for pagination" />
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107 </when>
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108 <when value="from_templates_summary">
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109 <param name="template_id" type="text" label="Template ID">
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110 <validator type="empty_field" message="Template ID is required" />
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111 </param>
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112 </when>
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113 <when value="from_templates_sources">
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114 <param name="template_id" type="text" label="Template ID">
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115 <validator type="empty_field" message="Template ID is required" />
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116 </param>
0
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117 </when>
4
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118 <when value="from_templates_count">
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119 <param name="smarts" type="text" value="" label="Exact SMARTS">
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120 <sanitizer sanitize="false" />
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121 </param>
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122 <repeat name="rep_template_ids" title="Template">
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123 <param name="template_id" type="text" label="ID">
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124 <validator type="empty_field" message="Not empty" />
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125 </param>
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126 </repeat>
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127 <repeat name="rep_reaction_ids" title="Reaction">
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128 <param name="reaction_id" type="text" label="ID">
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129 <validator type="empty_field" message="Not empty" />
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130 </param>
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131 </repeat>
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132 <param name="from_datasets" type="select" multiple="False"
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133 label="Select a specific database">
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134 <option value="any" selected="True">Any</option>
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135 <option value="metanetx">MetaNetX</option>
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136 <option value="rhea">Rhea</option>
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137 <option value="uspto">USPTO</option>
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138 </param>
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139 <param name="from_chemical_domain" type="select" multiple="False"
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140 label="Chemical domain">
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141 <option value="any" selected="True">Any</option>
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142 <option value="biochem">Biochem</option>
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143 <option value="orgchem">Orgchem</option>
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144 </param>
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145 <param name="ec_number" type="text" value="" label="EC number to filter templates" />
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146 <param name="min_radius" type="integer" min="0" max="10" optional="True"
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147 label="Single radius filter" />
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148 <param name="from_valid" type="select" multiple="False" label="Filter by validity">
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149 <option value="true" selected="True">True</option>
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150 <option value="any">Any</option>
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151 <option value="false">False</option>
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152 </param>
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153 <param name="dedup" type="boolean" checked="True"
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154 label="By default deduplicated templates are returned" />
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155 </when>
0
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156 </conditional>
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157 </inputs>
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158 <outputs>
3
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159 <data name="output_json" format="json" label="${tool.name}" />
0
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160 </outputs>
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161 <tests>
3
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162 <!-- Templates -->
0
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163 <test>
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164 <conditional name="cond_src">
3
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165 <param name="from_src" value="from_templates" />
4
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166 <param name="smarts" value="[O]-[C](=[O])" />
3
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167 <param name="limit" value="5" />
0
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168 </conditional>
3
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169 <output name="output_json" md5="0e4a782a2868c4b85a96f7c1d4ecaef8" />
0
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170 </test>
3
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171 <!-- Templates summary -->
0
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172 <test>
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173 <conditional name="cond_src">
3
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174 <param name="from_src" value="from_templates_summary" />
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175 <param name="template_id" value="RR:03-27BC85-19184A-A71018" />
0
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176 </conditional>
3
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177 <output name="output_json" md5="8cde1ac45b324c9893f70254587feb30" />
0
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178 </test>
3
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179 <!-- Templates sources -->
0
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180 <test>
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181 <conditional name="cond_src">
3
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182 <param name="from_src" value="from_templates_sources" />
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183 <param name="template_id" value="RR:03-27BC85-19184A-A71018" />
0
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184 </conditional>
3
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185 <output name="output_json" md5="33768abfc48aa896bfdfb736a3001950" />
0
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186 </test>
4
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187 <!-- Templates count -->
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188 <test>
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189 <conditional name="cond_src">
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190 <param name="from_src" value="from_templates_count" />
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191 <param name="smarts" value="[O]-[C](=[O])" />
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192 </conditional>
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193 <output name="output_json" md5="375fc61f8b47a81687dc567d3501f921" />
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194 </test>
0
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195 </tests>
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196 <help><![CDATA[
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197 RetroRules
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198 ==========
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199
3
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200 Querying the `RetroRules <https://retrorules.org/>`_ REST API
0
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201 ]]></help>
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202 <creator>
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203 <organization name="BioRetroSynth" url="https://github.com/brsynth" />
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204 </creator>
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205 <citations>
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206 <citation type="doi">10.1093/nar/gky940</citation>
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207 </citations>
3
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208 </tool>