| New set of Picard wrappers that do not rely on external scripts and deal with all aspects of picard management and UI via tool XML.
To modify and comment please submit pull requests to https://github.com/nekrut/picard |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/picard_plus
| Repository package_picard_122 revision 53eab8b10cfc owned by devteam |
| Name | Version | Type | |
|---|---|---|---|
| picard | 1.122.0 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| merge alignment data with additional info stored in an unmapped BAM dataset | 1.122.0 | any | |
| Downsample a file to retain a subset of the reads | 1.122.0 | any | |
| writes a file containing summary alignment metrics | 1.122.0 | any | |
| convert coordinate data into picard interval list format | 1.122.0 | any | |
| add or replaces read group information | 1.122.0 | any | |
| plots distribution of insert sizes | 1.122.0 | any | |
| chart distribution of base qualities | 1.122.0 | any | |
| revert SAM/BAM datasets to a previous state | 1.122.0 | any | |
| convert Fastq data into unaligned BAM | 1.122.0 | any | |
| sort SAM/BAM dataset | 1.122.0 | any | |
| compute metrics for evaluating of whole genome sequencing experiments | 1.121.0 | any | |
| ensure that all mate-pair information is in sync between each read and it's mate pair | 1.122.0 | any | |
| add comments to BAM dataset | 1.122.0 | any | |
| include or exclude aligned and unaligned reads and read lists | 1.122.0 | any | |
| normalize fasta datasets | 1.122.0 | any | |
| assess sequence library complexity from read sequences | 1.122.0 | any | |
| perform SAM/BAM grooming | 1.122.0 | any | |
| collect metrics about the alignment of RNA to various functional classes of loci in the genome | 1.122.0 | any | |
| charts the GC bias metrics | 1.122.0 | any | |
| replace header in a SAM/BAM dataset | 1.122.0 | any | |
| merges multiple SAM/BAM datasets into one | 1.122.0 | any | |
| charts the nucleotide distribution per cycle in a SAM or BAM dataset | 1.122.0 | any | |
| revert the original base qualities and add the mate cigar tag | 1.122.0 | any | |
| assess validity of SAM/BAM dataset | 1.122.0 | any | |
| extract reads and qualities from SAM/BAM dataset and convert to fastq | 1.122.0 | any | |
| reorder reads to match ordering in reference sequences | 1.122.0 | any | |
| examine aligned records in BAM datasets to locate duplicate molecules | 1.122.0 | any | |
| chart quality score distribution | 1.122.0 | any | |