Mercurial > repos > chrisd > coverage_sampler

comparison coverage_sampler.xml @ 25:99d75ed267fd draft

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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
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24:750a09c9cca2 25:99d75ed267fd
67 67
68 ------ 68 ------
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 Options: -q INT mask bases with quality lower than INT [0]
73 of five tells the program to begin by taking five percent of alignments from the alignment file. 73 -X INT mask bases with quality higher than INT [255]
74 74
75 max This parameter specifies the ending sample level for the program. 75 Options: -min INT Starting level to sample reads from (level is in percent)
76 76 -max INT Ending level to sample reads from (level is in percent)
77 skip This parameter specifies the amount of levels to skip between min and max. For example, 77 -skip INT Number of levels to skip
78 if you specify a min value of five, a max value of 100, and a skip value of five, then 78 -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output)
79 you would be sampling alignments in intervals of five. 79 -samples INT Number of iterations per sample level
80
81 t This parameter specifies a threshold value. Only genes having a gene fraction greater than
82 this value are provided as output.
83
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.
86 80
87 ------ 81 ------
88 82
89 **Output** 83 **Output**
90 84
91 Output of this program is a tab delimited text file with following: 85 Output of this program is a tab delimited text file with following:
92 86
93 Column Description 87 Column Description
94 Level The sampling level alignments were taken at 88 Level The sampling level alignments were taken at
95 Iteration The ith iteration of the current sampling level 89 Iteration The ith iteration of the current sampling level
96 Gene Id The reference sequence having a gene fraction greater than threshold 90 Gene Id The reference sequence having a gene fraction greater than threshold
97 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments 91 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments
98 Hits The amount of times that the reference sequence was seen from the sample of alignments 92 Hits The amount of times that the reference sequence was seen from the sample of alignments
99 93
100 ------ 94 ------
101 95
102 **Development** 96 **Development**
103 97
104 Development is being done on github_ 98 Development is being done on github_
105 99
106 .. _github: https://github.com/cdeanj/coverage_sampler 100 .. _github: https://github.com/cdeanj/coverage_sampler
107 101
108 ]]> 102 ]]></help>
109 </help>
110 <citations> 103 <citations>
111 </citations> 104 </citations>
112 </tool> 105 </tool>