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mvdbeek
e46f9e789c
This tool converts sample sheet collections back to their corresponding non-sample-sheet types by stripping the column_definitions and row column metadata: - sample_sheet -> list - sample_sheet:paired -> list:paired - sample_sheet:paired_or_unpaired -> list:paired_or_unpaired - sample_sheet:record -> list:record Useful when a sample sheet needs to be passed to a tool that expects a regular list collection, or when discarding sample sheet metadata.
53 lines
1.7 KiB
XML
53 lines
1.7 KiB
XML
<tool id="__CONVERT_SAMPLE_SHEET__"
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name="Convert sample sheet"
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version="1.0.0"
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tool_type="convert_sample_sheet">
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<description>to list collection</description>
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<type class="ConvertSampleSheetTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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<edam_operations>
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<edam_operation>operation_2409</edam_operation>
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</edam_operations>
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<macros>
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<import>model_operation_macros.xml</import>
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</macros>
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<inputs>
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<param type="data_collection" collection_type="sample_sheet,sample_sheet:paired,sample_sheet:paired_or_unpaired,sample_sheet" name="input" label="Sample sheet to convert" />
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</inputs>
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<outputs>
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<!-- type_source is a lie, we don't have a way to encode the transform that is actually happening -->
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<collection name="output" format_source="input" type_source="input" label="${on_string} (converted)" >
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</collection>
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</outputs>
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<help><![CDATA[
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========
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Synopsis
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========
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Converts a sample sheet collection back to its corresponding list collection type.
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===========
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Description
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===========
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This tool takes a sample sheet collection and produces a regular list collection, removing all sample sheet metadata (column definitions and row values).
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The conversion follows this mapping:
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- ``sample_sheet`` becomes ``list``
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- ``sample_sheet:paired`` becomes ``list:paired``
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- ``sample_sheet:paired_or_unpaired`` becomes ``list:paired_or_unpaired``
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Use this tool when you need to pass a sample sheet to a tool that expects a regular list collection, or when you want to discard the sample sheet metadata.
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----
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.. class:: infomark
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@QUOTA_USAGE_NOTE@
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]]></help>
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</tool>
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