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S4 class #6

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JulFrey wants to merge 5 commits into from
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S4 class #6

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b784061
start implementing an s4 class for pipeable workflows
Jan 22, 2026
a7f4622
adding s4 methods for single tool invocations
Jan 22, 2026
1044db7
debug run_tool
Jan 22, 2026
acc7b9d
add better tool and workflow input handling and validation
Jan 23, 2026
3063ebf
now handing over parameterst to tools in workflows possible download …
Jan 23, 2026
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1 change: 1 addition & 0 deletions GalaxyR.Rproj
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Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,5 @@ LineEndingConversion: Posix
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageCheckArgs: --no-examples
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Copilot AI Jan 23, 2026

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Adding --no-examples to PackageCheckArgs disables running examples during R CMD check. This can hide broken examples and reduce the quality assurance provided by the check process. Unless there's a specific reason to skip example checks (such as requiring unavailable external resources), consider removing this flag or ensuring all examples are properly wrapped in \dontrun{} or \donttest{} where appropriate.

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PackageCheckArgs: --no-examples
PackageCheckArgs:

Copilot uses AI. Check for mistakes.
PackageRoxygenize: rd,collate,namespace
18 changes: 10 additions & 8 deletions NAMESPACE
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@@ -1,11 +1,12 @@
# Generated by roxygen2: do not edit by hand

export(galaxy)
export(galaxy_delete_dataset)
export(galaxy_delete_datasets)
export(galaxy_download_result)
export(galaxy_get_file_info)
export(galaxy_get_tool)
export(galaxy_get_tool_id)
export(galaxy_get_workflow)
export(galaxy_get_workflow_inputs)
export(galaxy_has_key)
export(galaxy_history_size)
Expand All @@ -14,15 +15,16 @@ export(galaxy_list_histories)
export(galaxy_list_invocations)
export(galaxy_list_tools)
export(galaxy_list_workflows)
export(galaxy_poll_workflow)
export(galaxy_run_tool)
export(galaxy_set_credentials)
export(galaxy_start_workflow)
export(galaxy_upload_ftp)
export(galaxy_upload_https)
export(galaxy_wait_for_job)
exportMethods(galaxy_download_result)
exportMethods(galaxy_initialize)
exportMethods(galaxy_poll_tool)
exportMethods(galaxy_poll_workflow)
exportMethods(galaxy_run_tool)
exportMethods(galaxy_start_workflow)
exportMethods(galaxy_upload_ftp)
exportMethods(galaxy_upload_https)
importFrom(httr,VERB)
importFrom(httr,add_headers)
importFrom(httr,content)
importFrom(httr,status_code)
importFrom(stats,setNames)
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