Mercurial > repos > chrisd > coverage_sampler
changeset 15:233b2d979df4 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
| author | chrisd |
|---|---|
| date | Wed, 29 Jun 2016 02:43:33 -0400 |
| parents | 53a59e1eaa73 |
| children | 94b6db9db63c |
| files | coverage_sampler.xml |
| diffstat | 1 files changed, 15 insertions(+), 11 deletions(-) [+] |
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--- a/coverage_sampler.xml Wed Jun 29 02:33:49 2016 -0400 +++ b/coverage_sampler.xml Wed Jun 29 02:43:33 2016 -0400 @@ -61,12 +61,10 @@ **Coverage sampler** -Coverage sampler_ is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes +Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene that was covered from a random sampling of alignments. -.. _Coverage sampler: https://github.com/cdeanj/coverage_sampler - ------ **Options** @@ -83,23 +81,29 @@ -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. + -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. ------ **Output** - Output of this program is a tab delimited text file with following: +Output of this program is a tab delimited text file with following: - 1 Level The sampling level alignments were taken at - 2 Iteration The ith iteration of the current sampling level - 3 Gene Id The reference sequence having a gene fraction greater than threshold - 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments - 5 Hits The amount of times that the reference sequence was seen from the sample of alignments + 1 Level The sampling level alignments were taken at + 2 Iteration The ith iteration of the current sampling level + 3 Gene Id The reference sequence having a gene fraction greater than threshold + 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments + 5 Hits The amount of times that the reference sequence was seen from the sample of alignments ------ +**Development** + +Development is being done on github_ + +.. _github: https://github.com/cdeanj/coverage_sampler + ]]> </help> <citations>