Mercurial > repos > tduigou > retrorules
changeset 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 | |
| files | generate_test.py retrorules.xml |
| diffstat | 2 files changed, 65 insertions(+), 12 deletions(-) [+] |
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--- a/generate_test.py Mon Sep 15 12:37:50 2025 +0000 +++ b/generate_test.py Mon Sep 15 12:57:08 2025 +0000 @@ -63,7 +63,7 @@ print("templates-count") smarts_str = "[O]-[C](=[O])" cmd = ["--input-smarts-str", smarts_str] - value = run_cmd(subcommand="templates", sub_cmd=cmd) + value = run_cmd(subcommand="templates-count", sub_cmd=cmd) print("Test:", " ".join(cmd), "md5:", value) print("=" * 50)
--- a/retrorules.xml Mon Sep 15 12:37:50 2025 +0000 +++ b/retrorules.xml Mon Sep 15 12:57:08 2025 +0000 @@ -1,12 +1,16 @@ -<tool id="retrorules" name="RetroRules" version="1.0+galaxy1" profile="21.09" license="MIT"> +<tool id="retrorules" name="RetroRules" version="1.0+galaxy2" profile="21.09" license="MIT"> <description>Querying the RetroRules REST API</description> <requirements> <requirement type="package" version="2">requests</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/'query.py - #if str($cond_src.from_src) == 'from_templates' - templates + #if str($cond_src.from_src) == 'from_templates' or str($cond_src.from_src) == 'from_templates_count' + #if str($cond_src.from_src) == 'from_templates' + templates + #elif str($cond_src.from_src) == 'from_templates_count' + templates-count + #end if --input-smarts-str '$cond_src.smarts' #set template_ids = [] #for $x in $cond_src.rep_template_ids @@ -34,11 +38,13 @@ #set dedup = 'true' #end if --input-dedup-str $dedup - #if str($cond_src.limit) != '' - --input-limit-int '$cond_src.limit' - #end if - #if str($cond_src.offset) != '' - --input-offset-int '$cond_src.offset' + #if str($cond_src.from_src) == 'from_templates' + #if str($cond_src.limit) != '' + --input-limit-int '$cond_src.limit' + #end if + #if str($cond_src.offset) != '' + --input-offset-int '$cond_src.offset' + #end if #end if #elif str($cond_src.from_src) == 'from_templates_summary' templates-summary @@ -51,10 +57,11 @@ ]]></command> <inputs> <conditional name="cond_src"> - <param name="from_src" type="select" label="Select entry point"> + <param name="from_src" type="select" multiple="False" label="Select entry point"> <option value="from_templates" selected="True">Search templates</option> <option value="from_templates_summary">Summarize a template</option> <option value="from_templates_sources">List source reactions for a template</option> + <option value="from_templates_count">Count templates</option> </param> <when value="from_templates"> <param name="smarts" type="text" value="" label="Exact SMARTS"> @@ -92,7 +99,7 @@ <option value="false">False</option> </param> <param name="dedup" type="boolean" checked="True" - label="By default deduplicated templates are returne" /> + label="By default deduplicated templates are returned" /> <param name="limit" type="integer" min="1" optional="True" label="Limit number of returned templates" /> <param name="offset" type="integer" min="0" optional="True" @@ -108,6 +115,44 @@ <validator type="empty_field" message="Template ID is required" /> </param> </when> + <when value="from_templates_count"> + <param name="smarts" type="text" value="" label="Exact SMARTS"> + <sanitizer sanitize="false" /> + </param> + <repeat name="rep_template_ids" title="Template"> + <param name="template_id" type="text" label="ID"> + <validator type="empty_field" message="Not empty" /> + </param> + </repeat> + <repeat name="rep_reaction_ids" title="Reaction"> + <param name="reaction_id" type="text" label="ID"> + <validator type="empty_field" message="Not empty" /> + </param> + </repeat> + <param name="from_datasets" type="select" multiple="False" + label="Select a specific database"> + <option value="any" selected="True">Any</option> + <option value="metanetx">MetaNetX</option> + <option value="rhea">Rhea</option> + <option value="uspto">USPTO</option> + </param> + <param name="from_chemical_domain" type="select" multiple="False" + label="Chemical domain"> + <option value="any" selected="True">Any</option> + <option value="biochem">Biochem</option> + <option value="orgchem">Orgchem</option> + </param> + <param name="ec_number" type="text" value="" label="EC number to filter templates" /> + <param name="min_radius" type="integer" min="0" max="10" optional="True" + label="Single radius filter" /> + <param name="from_valid" type="select" multiple="False" label="Filter by validity"> + <option value="true" selected="True">True</option> + <option value="any">Any</option> + <option value="false">False</option> + </param> + <param name="dedup" type="boolean" checked="True" + label="By default deduplicated templates are returned" /> + </when> </conditional> </inputs> <outputs> @@ -118,7 +163,7 @@ <test> <conditional name="cond_src"> <param name="from_src" value="from_templates" /> - <param name="smarts" value="O]-[C](=[O])" /> + <param name="smarts" value="[O]-[C](=[O])" /> <param name="limit" value="5" /> </conditional> <output name="output_json" md5="0e4a782a2868c4b85a96f7c1d4ecaef8" /> @@ -139,6 +184,14 @@ </conditional> <output name="output_json" md5="33768abfc48aa896bfdfb736a3001950" /> </test> + <!-- Templates count --> + <test> + <conditional name="cond_src"> + <param name="from_src" value="from_templates_count" /> + <param name="smarts" value="[O]-[C](=[O])" /> + </conditional> + <output name="output_json" md5="375fc61f8b47a81687dc567d3501f921" /> + </test> </tests> <help><![CDATA[ RetroRules