Mercurial > repos > chrisd > coverage_sampler
changeset 18:9dd9da093f21 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit dac82c7c7880aa81a3a0875850854f2405b44dd5-dirty
| author | chrisd |
|---|---|
| date | Wed, 29 Jun 2016 02:57:50 -0400 |
| parents | bce433e42d1e |
| children | 246302afd481 |
| files | coverage_sampler.xml |
| diffstat | 1 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/coverage_sampler.xml Wed Jun 29 02:52:17 2016 -0400 +++ b/coverage_sampler.xml Wed Jun 29 02:57:50 2016 -0400 @@ -69,20 +69,20 @@ **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. + -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. + -max This parameter specifies the ending sample level for the program. - -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. + -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. + -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. ------ @@ -90,15 +90,15 @@ Output of this program is a tab delimited text file with following: -1 Level The sampling level alignments were taken at + Level The sampling level alignments were taken at -2 Iteration The ith iteration of the current sampling level + Iteration The ith iteration of the current sampling level -3 Gene Id The reference sequence having a gene fraction greater than threshold + 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 + 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 + Hits The amount of times that the reference sequence was seen from the sample of alignments ------