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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
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14:53a59e1eaa73 15:233b2d979df4
59 <help> 59 <help>
60 <![CDATA[ 60 <![CDATA[
61 61
62 **Coverage sampler** 62 **Coverage sampler**
63 63
64 Coverage sampler_ is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes 64 Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes
65 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 65 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
66 that was covered from a random sampling of alignments. 66 that was covered from a random sampling of alignments.
67
68 .. _Coverage sampler: https://github.com/cdeanj/coverage_sampler
69 67
70 ------ 68 ------
71 69
72 **Options** 70 **Options**
73 71
81 you would be sampling alignments in intervals of five. 79 you would be sampling alignments in intervals of five.
82 80
83 -t This parameter specifies a threshold value. Only genes having a gene fraction greater than 81 -t This parameter specifies a threshold value. Only genes having a gene fraction greater than
84 this value are provided as output. 82 this value are provided as output.
85 83
86 -samples This parameter specifies the amount of iterations you would like to sample at. For example, a 84 -samples This parameter specifies the amount of iterations you would like to sample at. For example,
87 sample value of five would sample each level five times. 85 a sample value of five would sample each level five times.
88 86
89 ------ 87 ------
90 88
91 **Output** 89 **Output**
92 90
93 Output of this program is a tab delimited text file with following: 91 Output of this program is a tab delimited text file with following:
94 92
95 1 Level The sampling level alignments were taken at 93 1 Level The sampling level alignments were taken at
96 2 Iteration The ith iteration of the current sampling level 94 2 Iteration The ith iteration of the current sampling level
97 3 Gene Id The reference sequence having a gene fraction greater than threshold 95 3 Gene Id The reference sequence having a gene fraction greater than threshold
98 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments 96 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments
99 5 Hits The amount of times that the reference sequence was seen from the sample of alignments 97 5 Hits The amount of times that the reference sequence was seen from the sample of alignments
100 98
101 ------ 99 ------
100
101 **Development**
102
103 Development is being done on github_
104
105 .. _github: https://github.com/cdeanj/coverage_sampler
102 106
103 ]]> 107 ]]>
104 </help> 108 </help>
105 <citations> 109 <citations>
106 </citations> 110 </citations>