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Sort BAM Files using SAMTools Sort.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
Custom directory

Specify the output directory.

Output BAM nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. 
Build indexBuild index for the sorted file with SAMTools index.human.hg18

Parameters in Workflow File 

Type: Sort-bam

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirOutput BAM namestring
out-nameOutput file namestring
indexBuild indexboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: BAM File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Sorted BAM File

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLurlstring
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