Mercurial > repos > chrisd > coverage_sampler
changeset 25:99d75ed267fd draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
| author | chrisd |
|---|---|
| date | Wed, 29 Jun 2016 03:42:00 -0400 |
| parents | 750a09c9cca2 |
| children | 89c934705f57 |
| files | coverage_sampler.xml |
| diffstat | 1 files changed, 11 insertions(+), 18 deletions(-) [+] |
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--- a/coverage_sampler.xml Wed Jun 29 03:24:38 2016 -0400 +++ b/coverage_sampler.xml Wed Jun 29 03:42:00 2016 -0400 @@ -69,20 +69,14 @@ **Options** -min This parameter specifies the starting sample level for the program. For example, a min value - of five tells the program to begin by taking five percent of alignments from the alignment file. - -max This parameter specifies the ending sample level for the program. +Options: -q INT mask bases with quality lower than INT [0] + -X INT mask bases with quality higher than INT [255] -skip This parameter specifies the amount of levels to skip between min and max. For example, - if you specify a min value of five, a max value of 100, and a skip value of five, then - you would be sampling alignments in intervals of five. - -t This parameter specifies a threshold value. Only genes having a gene fraction greater than - this value are provided as output. - -samples This parameter specifies the amount of iterations you would like to sample at. For example, - a sample value of five would sample each level five times. +Options: -min INT Starting level to sample reads from (level is in percent) + -max INT Ending level to sample reads from (level is in percent) + -skip INT Number of levels to skip + -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output) + -samples INT Number of iterations per sample level ------ @@ -91,11 +85,11 @@ Output of this program is a tab delimited text file with following: Column Description -Level The sampling level alignments were taken at +Level The sampling level alignments were taken at Iteration The ith iteration of the current sampling level -Gene Id The reference sequence having a gene fraction greater than threshold +Gene Id The reference sequence having a gene fraction greater than threshold Gene Fraction The overall fraction of the gene that was covered from the sample of alignments -Hits The amount of times that the reference sequence was seen from the sample of alignments +Hits The amount of times that the reference sequence was seen from the sample of alignments ------ @@ -105,8 +99,7 @@ .. _github: https://github.com/cdeanj/coverage_sampler -]]> - </help> + ]]></help> <citations> </citations> </tool>