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Merge pull request #11332 from simonbray/fix-run-tool

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[21.01] Submit input_format to tools API in payload, not as a parameter
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Marius van den Beek
2021-02-10 09:34:49 +01:00
committed by GitHub
parent b4c2ba47a3 33035a022f
commit 2e506e41a8
1 changed files with 7 additions and 3 deletions
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lib/galaxy/webapps/galaxy/api/tools.py
+7 -3
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@@ -486,8 +486,12 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
POST /api/tools
Execute tool with a given parameter payload
:param input_format: input format for the payload. Possible values are the default 'legacy' (where inputs nested inside conditionals or repeats are identified with e.g. '<conditional_name>|<input_name>') or '21.01' (where inputs inside conditionals or repeats are nested elements).
:type input_format: string
:param input_format: input format for the payload. Possible values are
the default 'legacy' (where inputs nested inside conditionals or
repeats are identified with e.g. '<conditional_name>|<input_name>') or
'21.01' (where inputs inside conditionals or repeats are nested
elements).
:type input_format: str
"""
tool_id = payload.get("tool_id")
tool_uuid = payload.get("tool_uuid")
@@ -559,7 +563,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
# as a regular tool parameter we accept both.
use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false'))
input_format = kwd.get('input_format', 'legacy')
input_format = str(payload.get('input_format', 'legacy'))
vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)