Nate Coraor 3fc4c7c4f8 Enable the ftype attribute for test outputs, fixes the sam-to-bam test.

2011-03-01 15:46:35 -05:00

..

bam_to_sam.py

Added version info to stdout for NGS tools

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

bam_to_sam.xml

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -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

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

sam2interval.py

Have sam2interval provide a (partial) header so that strand is automatically set in metadata.

2010-02-05 11:53:06 -05:00

sam2interval.xml

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

sam_bitwise_flag_filter.py

Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria

2010-11-13 14:37:26 -05:00

sam_bitwise_flag_filter.xml

Minimally functional splitting.

2010-11-10 12:06:05 -05:00

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

Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper

2011-01-12 13:31:04 -05:00

sam_pileup.py

Added version info to stdout for NGS tools

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

sam_pileup.xml

Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper

2011-01-12 13:31:04 -05:00

sam_to_bam.py

Added version info to stdout for NGS tools

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

sam_to_bam.xml

Enable the ftype attribute for test outputs, fixes the sam-to-bam test.

2011-03-01 15:46:35 -05:00

samtools_flagstat.xml

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00