between assemblies and genomes
liftOver_wrapper.py
$input
"$out_file1"
"$out_file2"
$dbkey
$to_dbkey
#if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) or isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gtf').__class__):
"gff"
#else:
"interval"
#end if
$minMatch ${multiple.choice} ${multiple.minChainT} ${multiple.minChainQ} ${multiple.minSizeQ}
ucsc_tools
.. class:: warningmark
Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).
.. class:: warningmark
This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,
start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
and track and browser lines will be ignored, but if other non-interval lines
are present the tool will return empty output datasets.
-----
.. class:: infomark
**What it does**
This tool is based on the LiftOver utility and Chain track from `the UC Santa Cruz Genome Browser`__.
It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.
.. __: http://genome.ucsc.edu/
-----
**Example**
Converting the following hg16 intervals to hg18 intervals::
chrX 85170 112199 AK002185 0 +
chrX 110458 112199 AK097346 0 +
chrX 112203 121212 AK074528 0 -
will produce the following hg18 intervals::
chrX 132991 160020 AK002185 0 +
chrX 158279 160020 AK097346 0 +
chrX 160024 169033 AK074528 0 -