Mercurial > repos > chrisd > coverage_sampler

comparison coverage_sampler.xml @ 18:9dd9da093f21 draft

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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
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17:bce433e42d1e 18:9dd9da093f21
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69 69
70 **Options** 70 **Options**
71 71
72 -min This parameter specifies the starting sample level for the program. For example, a min value 72 -min This parameter specifies the starting sample level for the program. For example, a min value
73 of five tells the program to begin by taking five percent of alignments from the alignment file. 73 of five tells the program to begin by taking five percent of alignments from the alignment file.
74 74
75 -max This parameter specifies the ending sample level for the program. 75 -max This parameter specifies the ending sample level for the program.
76 76
77 -skip This parameter specifies the amount of levels to skip between min and max. For example, 77 -skip This parameter specifies the amount of levels to skip between min and max. For example,
78 if you specify a min value of five, a max value of 100, and a skip value of five, then 78 if you specify a min value of five, a max value of 100, and a skip value of five, then
79 you would be sampling alignments in intervals of five. 79 you would be sampling alignments in intervals of five.
80 80
81 -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
82 this value are provided as output. 82 this value are provided as output.
83 83
84 -samples This parameter specifies the amount of iterations you would like to sample at. For example, 84 -samples This parameter specifies the amount of iterations you would like to sample at. For example,
85 a sample value of five would sample each level five times. 85 a sample value of five would sample each level five times.
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89 **Output** 89 **Output**
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91 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:
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93 1 Level The sampling level alignments were taken at 93 Level The sampling level alignments were taken at
94 94
95 2 Iteration The ith iteration of the current sampling level 95 Iteration The ith iteration of the current sampling level
96 96
97 3 Gene Id The reference sequence having a gene fraction greater than threshold 97 Gene Id The reference sequence having a gene fraction greater than threshold
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99 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments 99 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments
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101 5 Hits The amount of times that the reference sequence was seen from the sample of alignments 101 Hits The amount of times that the reference sequence was seen from the sample of alignments
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105 **Development** 105 **Development**
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