Purpose

Reverts SAM or BAM files to a previous state by removing certain types of information and/or substituting in the original quality scores when available.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

SORT_ORDER=SortOrder
SO=SortOrder                  The sort order to create the reverted output file with.  Default value: queryname.
                              Possible values: {unsorted, queryname, coordinate}

RESTORE_ORIGINAL_QUALITIES=Boolean
OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.
                              Default value: true. Possible values: {true, false}

REMOVE_DUPLICATE_INFORMATION=Boolean
                              Remove duplicate read flags from all reads.  Note that if this is true and
                              REMOVE_ALIGNMENT_INFORMATION==false,  the output may have the unusual but sometimes
                              desirable trait of having unmapped reads that are marked as duplicates.  Default value:
                              true. Possible values: {true, false}

REMOVE_ALIGNMENT_INFORMATION=Boolean
                              Remove all alignment information from the file.  Default value: true. TPossible values: {true, false}

ATTRIBUTE_TO_CLEAR=String     When removing alignment information, the set of optional tags to remove.  This option may
                              be specified 0 or more times.

SANITIZE=Boolean              WARNING: This option is potentially destructive. If enabled will discard reads in order
                              to produce a consistent output BAM. Reads discarded include (but are not limited to)
                              paired reads with missing mates, duplicated records, records with mismatches in length of
                              bases and qualities. This option can only be enabled if the output sort order is
                              queryname and will always cause sorting to occur.  Possible values: {true, false}

MAX_DISCARD_FRACTION=Double   If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
                              sanitization thenthe program will exit with an Exception instead of exiting cleanly.
                              Output BAM will still be valid.  Default value: 0.01.

SAMPLE_ALIAS=String
ALIAS=String                  The sample alias to use in the reverted output file.  This will override the existing
                              sample alias in the file and is used only if all the read groups in the input file have
                              the same sample alias   Default value: null.

LIBRARY_NAME=String
LIB=String                    The library name to use in the reverted output file.  This will override the existing
                              sample alias in the file and is used only if all the read groups in the input file have
                              the same sample alias   Default value: null.

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .