Mercurial > repos > tduigou > retrorules
comparison retrorules.xml @ 4:bd5ffc799c16 draft default tip
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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| 3:cfa70e3fe1a4 | 4:bd5ffc799c16 |
|---|---|
| 1 <tool id="retrorules" name="RetroRules" version="1.0+galaxy1" profile="21.09" license="MIT"> | 1 <tool id="retrorules" name="RetroRules" version="1.0+galaxy2" profile="21.09" license="MIT"> |
| 2 <description>Querying the RetroRules REST API</description> | 2 <description>Querying the RetroRules REST API</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2">requests</requirement> | 4 <requirement type="package" version="2">requests</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 python '$__tool_directory__/'query.py | 7 python '$__tool_directory__/'query.py |
| 8 #if str($cond_src.from_src) == 'from_templates' | 8 #if str($cond_src.from_src) == 'from_templates' or str($cond_src.from_src) == 'from_templates_count' |
| 9 templates | 9 #if str($cond_src.from_src) == 'from_templates' |
| 10 templates | |
| 11 #elif str($cond_src.from_src) == 'from_templates_count' | |
| 12 templates-count | |
| 13 #end if | |
| 10 --input-smarts-str '$cond_src.smarts' | 14 --input-smarts-str '$cond_src.smarts' |
| 11 #set template_ids = [] | 15 #set template_ids = [] |
| 12 #for $x in $cond_src.rep_template_ids | 16 #for $x in $cond_src.rep_template_ids |
| 13 #silent template_ids.append(str($x.template_id)) | 17 #silent template_ids.append(str($x.template_id)) |
| 14 #end for | 18 #end for |
| 32 #set dedup = 'false' | 36 #set dedup = 'false' |
| 33 #if str($cond_src.dedup) == 'true' | 37 #if str($cond_src.dedup) == 'true' |
| 34 #set dedup = 'true' | 38 #set dedup = 'true' |
| 35 #end if | 39 #end if |
| 36 --input-dedup-str $dedup | 40 --input-dedup-str $dedup |
| 37 #if str($cond_src.limit) != '' | 41 #if str($cond_src.from_src) == 'from_templates' |
| 38 --input-limit-int '$cond_src.limit' | 42 #if str($cond_src.limit) != '' |
| 39 #end if | 43 --input-limit-int '$cond_src.limit' |
| 40 #if str($cond_src.offset) != '' | 44 #end if |
| 41 --input-offset-int '$cond_src.offset' | 45 #if str($cond_src.offset) != '' |
| 46 --input-offset-int '$cond_src.offset' | |
| 47 #end if | |
| 42 #end if | 48 #end if |
| 43 #elif str($cond_src.from_src) == 'from_templates_summary' | 49 #elif str($cond_src.from_src) == 'from_templates_summary' |
| 44 templates-summary | 50 templates-summary |
| 45 --input-template-id-str '$cond_src.template_id' | 51 --input-template-id-str '$cond_src.template_id' |
| 46 #elif str($cond_src.from_src) == 'from_templates_sources' | 52 #elif str($cond_src.from_src) == 'from_templates_sources' |
| 49 #end if | 55 #end if |
| 50 --output-data-json '$output_json' | 56 --output-data-json '$output_json' |
| 51 ]]></command> | 57 ]]></command> |
| 52 <inputs> | 58 <inputs> |
| 53 <conditional name="cond_src"> | 59 <conditional name="cond_src"> |
| 54 <param name="from_src" type="select" label="Select entry point"> | 60 <param name="from_src" type="select" multiple="False" label="Select entry point"> |
| 55 <option value="from_templates" selected="True">Search templates</option> | 61 <option value="from_templates" selected="True">Search templates</option> |
| 56 <option value="from_templates_summary">Summarize a template</option> | 62 <option value="from_templates_summary">Summarize a template</option> |
| 57 <option value="from_templates_sources">List source reactions for a template</option> | 63 <option value="from_templates_sources">List source reactions for a template</option> |
| 64 <option value="from_templates_count">Count templates</option> | |
| 58 </param> | 65 </param> |
| 59 <when value="from_templates"> | 66 <when value="from_templates"> |
| 60 <param name="smarts" type="text" value="" label="Exact SMARTS"> | 67 <param name="smarts" type="text" value="" label="Exact SMARTS"> |
| 61 <sanitizer sanitize="false" /> | 68 <sanitizer sanitize="false" /> |
| 62 </param> | 69 </param> |
| 90 <option value="true" selected="True">True</option> | 97 <option value="true" selected="True">True</option> |
| 91 <option value="any">Any</option> | 98 <option value="any">Any</option> |
| 92 <option value="false">False</option> | 99 <option value="false">False</option> |
| 93 </param> | 100 </param> |
| 94 <param name="dedup" type="boolean" checked="True" | 101 <param name="dedup" type="boolean" checked="True" |
| 95 label="By default deduplicated templates are returne" /> | 102 label="By default deduplicated templates are returned" /> |
| 96 <param name="limit" type="integer" min="1" optional="True" | 103 <param name="limit" type="integer" min="1" optional="True" |
| 97 label="Limit number of returned templates" /> | 104 label="Limit number of returned templates" /> |
| 98 <param name="offset" type="integer" min="0" optional="True" | 105 <param name="offset" type="integer" min="0" optional="True" |
| 99 label="Offset for pagination" /> | 106 label="Offset for pagination" /> |
| 100 </when> | 107 </when> |
| 105 </when> | 112 </when> |
| 106 <when value="from_templates_sources"> | 113 <when value="from_templates_sources"> |
| 107 <param name="template_id" type="text" label="Template ID"> | 114 <param name="template_id" type="text" label="Template ID"> |
| 108 <validator type="empty_field" message="Template ID is required" /> | 115 <validator type="empty_field" message="Template ID is required" /> |
| 109 </param> | 116 </param> |
| 117 </when> | |
| 118 <when value="from_templates_count"> | |
| 119 <param name="smarts" type="text" value="" label="Exact SMARTS"> | |
| 120 <sanitizer sanitize="false" /> | |
| 121 </param> | |
| 122 <repeat name="rep_template_ids" title="Template"> | |
| 123 <param name="template_id" type="text" label="ID"> | |
| 124 <validator type="empty_field" message="Not empty" /> | |
| 125 </param> | |
| 126 </repeat> | |
| 127 <repeat name="rep_reaction_ids" title="Reaction"> | |
| 128 <param name="reaction_id" type="text" label="ID"> | |
| 129 <validator type="empty_field" message="Not empty" /> | |
| 130 </param> | |
| 131 </repeat> | |
| 132 <param name="from_datasets" type="select" multiple="False" | |
| 133 label="Select a specific database"> | |
| 134 <option value="any" selected="True">Any</option> | |
| 135 <option value="metanetx">MetaNetX</option> | |
| 136 <option value="rhea">Rhea</option> | |
| 137 <option value="uspto">USPTO</option> | |
| 138 </param> | |
| 139 <param name="from_chemical_domain" type="select" multiple="False" | |
| 140 label="Chemical domain"> | |
| 141 <option value="any" selected="True">Any</option> | |
| 142 <option value="biochem">Biochem</option> | |
| 143 <option value="orgchem">Orgchem</option> | |
| 144 </param> | |
| 145 <param name="ec_number" type="text" value="" label="EC number to filter templates" /> | |
| 146 <param name="min_radius" type="integer" min="0" max="10" optional="True" | |
| 147 label="Single radius filter" /> | |
| 148 <param name="from_valid" type="select" multiple="False" label="Filter by validity"> | |
| 149 <option value="true" selected="True">True</option> | |
| 150 <option value="any">Any</option> | |
| 151 <option value="false">False</option> | |
| 152 </param> | |
| 153 <param name="dedup" type="boolean" checked="True" | |
| 154 label="By default deduplicated templates are returned" /> | |
| 110 </when> | 155 </when> |
| 111 </conditional> | 156 </conditional> |
| 112 </inputs> | 157 </inputs> |
| 113 <outputs> | 158 <outputs> |
| 114 <data name="output_json" format="json" label="${tool.name}" /> | 159 <data name="output_json" format="json" label="${tool.name}" /> |
| 116 <tests> | 161 <tests> |
| 117 <!-- Templates --> | 162 <!-- Templates --> |
| 118 <test> | 163 <test> |
| 119 <conditional name="cond_src"> | 164 <conditional name="cond_src"> |
| 120 <param name="from_src" value="from_templates" /> | 165 <param name="from_src" value="from_templates" /> |
| 121 <param name="smarts" value="O]-[C](=[O])" /> | 166 <param name="smarts" value="[O]-[C](=[O])" /> |
| 122 <param name="limit" value="5" /> | 167 <param name="limit" value="5" /> |
| 123 </conditional> | 168 </conditional> |
| 124 <output name="output_json" md5="0e4a782a2868c4b85a96f7c1d4ecaef8" /> | 169 <output name="output_json" md5="0e4a782a2868c4b85a96f7c1d4ecaef8" /> |
| 125 </test> | 170 </test> |
| 126 <!-- Templates summary --> | 171 <!-- Templates summary --> |
| 136 <conditional name="cond_src"> | 181 <conditional name="cond_src"> |
| 137 <param name="from_src" value="from_templates_sources" /> | 182 <param name="from_src" value="from_templates_sources" /> |
| 138 <param name="template_id" value="RR:03-27BC85-19184A-A71018" /> | 183 <param name="template_id" value="RR:03-27BC85-19184A-A71018" /> |
| 139 </conditional> | 184 </conditional> |
| 140 <output name="output_json" md5="33768abfc48aa896bfdfb736a3001950" /> | 185 <output name="output_json" md5="33768abfc48aa896bfdfb736a3001950" /> |
| 186 </test> | |
| 187 <!-- Templates count --> | |
| 188 <test> | |
| 189 <conditional name="cond_src"> | |
| 190 <param name="from_src" value="from_templates_count" /> | |
| 191 <param name="smarts" value="[O]-[C](=[O])" /> | |
| 192 </conditional> | |
| 193 <output name="output_json" md5="375fc61f8b47a81687dc567d3501f921" /> | |
| 141 </test> | 194 </test> |
| 142 </tests> | 195 </tests> |
| 143 <help><![CDATA[ | 196 <help><![CDATA[ |
| 144 RetroRules | 197 RetroRules |
| 145 ========== | 198 ========== |