Mercurial > repos > fubar > genomic_association_tester
changeset 6:f118c5b066a0 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 28 Aug 2013 02:47:05 -0400 |
| parents | 99f146c2d943 |
| children | 453d54adbc51 |
| files | rlGAT/rlGAT.xml |
| diffstat | 1 files changed, 16 insertions(+), 13 deletions(-) [+] |
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--- a/rlGAT/rlGAT.xml Wed Aug 28 00:50:53 2013 -0400 +++ b/rlGAT/rlGAT.xml Wed Aug 28 02:47:05 2013 -0400 @@ -37,7 +37,7 @@ <param name="title" label="Name for this job's output file" type="text" size="80" value="GAT"/> <param name="numsamp" type="integer" value="1000" size="5" label="Number of simulations - longer takes longer - 1000 is usually a reasonable choice" /> <param name="counter" type="select" label="Counting methods to use - multiple will generate multiple output files" multiple="True" - help="Use ctrl to select multiple counters. If in doubt, read the fine manual"> + help="CURRENTLY ONLY DEFAULT AVAILABLE! Soon - Use ctrl to select multiple counters. If in doubt, read the fine manual"> <option value="nucleotide-overlap" selected="true">nucleotide-overlap: number of bases overlapping</option> <option value="segment-overlap">segment-overlap: number of intervals intervals in the segments of interest overlapping annotations. A single base-pair overlap is sufficient</option> <option value="segment-mid-overlap">segment-mid-overlap: number of intervals in the segments of interest overlapping at their midpoint annotations</option> @@ -105,31 +105,34 @@ The gat tool requires the following input: - A set of intervals S with segments of interest to test + * A set of intervals S with segments of interest to test - A set of intervals A with annotations to test against + * A set of intervals A with annotations to test against - A set of intervals W describing a workspace + * A set of intervals W describing a workspace All of the options –segment-file, –workspace-file, –annotation-file can be used several times on the command line. What happens with multiple files depends on the file type: -Multiple –segment-file entries are added to the list of segments of interest to test with. -Multiple –annotation-file entries are added to the list of annotations to test against. -Multiple –workspace entries are intersected to create a single workspace. -Generally, gat will test m segments of interest lists against n annotations lists in all m * n combinations. - -Within a bed formatted file, different tracks can be separated using a UCSC formatted track line, such as this: + * Multiple –segment-file entries are added to the list of segments of interest to test with. + + * Multiple –annotation-file entries are added to the list of annotations to test against. + + * Multiple –workspace entries are intersected to create a single workspace. + + * Generally, gat will test m segments of interest lists against n annotations lists in all m * n combinations. - track name="segmentset1" +Within a bed formatted file, different tracks can be separated using a UCSC formatted track line, such as this:: + + track name="segmentset1" chr1 23 100 chr3 50 2000 track name="segmentset2" chr1 1000 2000 chr3 4000 5000 -or alternatively, using the fourth column in a bed formatted file: +or alternatively, using the fourth column in a bed formatted file:: chr1 23 100 segmentset1 chr3 50 2000 segmentset1 @@ -138,7 +141,7 @@ The latter takes precedence. The option –ignore-segment-tracks forces gat to ignore the fourth column and consider all intervals to be from a single interval set. -Note Be careful with bed-files where each interval gets a unique identifier. Gat will interprete each interval as a separate segment set to read. +*Note* Be careful with bed-files where each interval gets a unique identifier. Gat will interprete each interval as a separate segment set to read. This is usually not intended and causes gat to require a very large amount of memory. By default, tracks can not be split over multiple files.