{"type":"doc","content":[{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"include","parameters":{"macroParams":{"":{"value":"docs:_DE_archived_apps_blurb"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Include Page"}}}},{"type":"paragraph","content":[{"text":" ","type":"text"}]},{"type":"paragraph","content":[{"text":" ","type":"text"},{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"cxhtml":"INLINEStaff

GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

BEDTools shuffleBed

Community rating: ?????

Randomly permute the locations of a feature file among a genome

Quick Start

To use BEDTools shuffleBed, import your data in BED format.
Resources: http://code.google.com/p/bedtools/

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Bedtools.

Input File(s)

Use b.bed and my.genome from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Default parameters only, no further configuration needed.

Output File(s)

Expect bedtools_shuffle_output as output.

Tool Source for App

http://code.google.com/p/bedtools/

","nestedContent":{"type":"doc","content":[{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"show-if","parameters":{"macroParams":{"atlassian-macro-output-type":{"value":"INLINE"},"group":{"value":"Staff"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"show-if"}}},"content":[{"type":"table","attrs":{"layout":"default"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"background":"Orange","rowspan":1},"content":[{"type":"paragraph","content":[{"text":"VISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"Gainsboro","rowspan":1},"content":[{"type":"heading","attrs":{"level":1},"content":[{"text":"BEDTools shuffleBed","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"paragraph","content":[{"text":"Community rating: ?????","type":"text"}]},{"type":"paragraph","content":[{"text":"Randomly permute the locations of a feature file among a genome","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To use ","type":"text"},{"text":"BEDTools shuffleBed","type":"text","marks":[{"type":"strong"}]},{"text":", import your d","type":"text"},{"text":"ata in BED format.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Resources:","type":"text","marks":[{"type":"strong"}]},{"text":" ","type":"text"},{"text":"http://code.google.com/p/bedtools/","type":"text","marks":[{"type":"link","attrs":{"href":"http://code.google.com/p/bedtools/"}},{"type":"textColor","attrs":{"color":"#800080"}}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Test data for this app appears directly in the Discovery Environment in the Data window under ","type":"text"},{"text":"Community Data -> iplantcollaborative -> e","type":"text","marks":[{"type":"em"}]},{"text":"xample_data ->","type":"text","marks":[{"type":"em"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":" ","type":"text"},{"text":"Bedtools","type":"text","marks":[{"type":"em"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":".","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Use","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":" ","type":"text"},{"text":"b.bed","type":"text","marks":[{"type":"strong"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":" ","type":"text"},{"text":"and","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":" ","type":"text"},{"text":"my.genome","type":"text","marks":[{"type":"strong"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":" ","type":"text"},{"text":"from the direct","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"ory above as test input.","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"paragraph","content":[{"text":"When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Default parameters only, no further configuration needed.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Expect bedtools_shuffle_output as output.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Tool Source for App","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://code.google.com/p/bedtools/","type":"text","marks":[{"type":"link","attrs":{"href":"http://code.google.com/p/bedtools/"}},{"type":"textColor","attrs":{"color":"#800080"}}]}]}]}]}]}]}]}]}],"version":1}}}}]}],"version":1}

BEDTools shuffleBed (archived)