Jeremy Goecks 72f6f87644 Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

..

bam_to_sam.py

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

bam_to_sam.xml

Update help for some SAMTools.

2011-11-21 16:55:16 -05:00

pileup_interval.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

pileup_interval.xml

Requirements tags for some samtools tools

2010-09-26 18:06:01 -04:00

pileup_parser.pl

Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.

2010-04-14 13:52:35 -04:00

pileup_parser.xml

Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

sam2interval.py

sam2interval: Add read_name column

2011-08-24 16:43:02 -04:00

sam2interval.xml

Fix to sam2interval bug reported by Kathy So. The bug was causing sam2interval to successfully parse unmapped sam entries, which have no valid coordinate.

2011-06-10 14:42:41 -04:00

sam_bitwise_flag_filter.py

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

sam_bitwise_flag_filter.xml

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

sam_merge_code.py

Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

2010-09-27 21:35:03 -04:00

sam_merge.py

Added version info to stdout for NGS tools

2010-11-24 12:35:49 -05:00

sam_merge.xml

Merged sam_merge fixes from galaxy-central keeping change to set TMP_DIR

2011-12-22 11:13:07 -05:00

sam_pileup.py

Added version info to stdout for NGS tools

2010-11-24 12:35:49 -05:00

sam_pileup.xml

The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.

2011-12-06 11:42:12 -05:00

sam_to_bam.py

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

sam_to_bam.xml

Update help for some SAMTools.

2011-11-21 16:55:16 -05:00

samtools_flagstat.xml

Update help for some SAMTools.

2011-11-21 16:55:16 -05:00

samtools_mpileup.xml

Fix inconsequential warning about when tag when loading samtools mpileup.

2012-04-10 16:07:19 -04:00

samtools_rmdup.xml

Update help for some SAMTools.

2011-11-21 16:55:16 -05:00

samtools_slice_bam.py

Add Slice BAM by regions tool.

2012-05-02 11:32:19 -04:00

samtools_slice_bam.xml

Fix typo in BAM slice tool.

2012-05-02 11:47:04 -04:00

samtools_wrapper.py

Add SAMTools mpileup.

2011-11-21 16:30:34 -05:00