Mercurial > repos > chrisd > coverage_sampler
changeset 14:53a59e1eaa73 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
author | chrisd |
---|---|
date | Wed, 29 Jun 2016 02:33:49 -0400 |
parents | 65d8343a6122 |
children | 233b2d979df4 |
files | coverage_sampler.xml |
diffstat | 1 files changed, 42 insertions(+), 15 deletions(-) [+] |
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--- a/coverage_sampler.xml Wed Jun 29 00:29:22 2016 -0400 +++ b/coverage_sampler.xml Wed Jun 29 02:33:49 2016 -0400 @@ -56,25 +56,52 @@ <output name="output" file="csa_no_result" ftype="tabular"/> </test> </tests> - <help><![CDATA[ -A simple tool for calculating the amount of a gene that is covered by a sample of alignments. + <help> +<![CDATA[ + +**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 +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. -Program: Coverage Sampler +.. _Coverage sampler: https://github.com/cdeanj/coverage_sampler + +------ -Contact: Chris Dean <cdean11@rams.colostate.edu> +**Options** -Usage: csa [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. + + -max This parameter specifies the ending sample level for the program. -Options: - -ref_fp STR/FILE ref file path - -sam_fp STR/FILE sam file path - -min INT starting sample level - -max INT ending sample level - -skip INT amount of sample levels to skip - -t INT gene fraction threshold - -samples INT iterations per sample level - -out_fp STR/FILE output file path - ]]></help> + -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. + + -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: + + 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 + +------ + +]]> + </help> <citations> </citations> </tool>