Mercurial > repos > greg > vsnp_statistics
changeset 2:7fe0cbb8c894 draft
Uploaded
author | greg |
---|---|
date | Thu, 30 Apr 2020 10:26:20 -0400 (2020-04-30) |
parents | 14e29f7d59ca |
children | 321a8259e3f9 |
files | .shed.yml vsnp_statistics.xml |
diffstat | 2 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/.shed.yml Wed Apr 29 16:56:10 2020 -0400 +++ b/.shed.yml Thu Apr 30 10:26:20 2020 -0400 @@ -1,10 +1,12 @@ name: vsnp_statistics owner: greg description: | - Contains a tool that outputs statistics on VCF files. + Contains a tool that produces an Excel spreadsheet containing statistics for samples and associated metrics files. homepage_url: https://github.com/USDA-VS/vSNP long_description: | - Contains a tool that outputs statistics on VCF files. + Contains a tool Accepts a single fastqsanger sample, a set of paired read samples, or a collections of samples + along with associated SAMtools idxstats and vSNP zero coverage metrics files and extracts information from them + to produce an Excel spreadsheet containing statistics for each sample. remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics type: unrestricted categories:
--- a/vsnp_statistics.xml Wed Apr 29 16:56:10 2020 -0400 +++ b/vsnp_statistics.xml Thu Apr 30 10:26:20 2020 -0400 @@ -1,7 +1,6 @@ <tool id="vsnp_statistics" name="vSNP: statistics" version="1.0.0"> <description></description> <requirements> - <requirement type="package" version="0.5.1">humanize</requirement> <requirement type="package" version="1.16.5">numpy</requirement> <requirement type="package" version="0.25.3">pandas</requirement> <requirement type="package" version="1.2.0">xlrd</requirement> @@ -122,10 +121,11 @@ <help> **What it does** -Accepts a single fastqsanger read, a set of paired reads, or a collections of reads along with associated SAMtools -idxstats and vSNP zero coverage metrics files and extracts information from the files to produce a tabular statistics -dataset that includes total reads, mean read length and quality, reads passing Q30, mapped and unmapped reads, depth -of coverage, good SNP count and more. +Accepts a single fastqsanger sample, a set of paired read samples, or a collections of samples along with associated +SAMtools idxstats and vSNP zero coverage metrics files and extracts information from them to produce an Excel +spreadsheet containing statistics for each sample. Statistics include reference, file size, mean read length, mean +read quality, reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, +reference with coverage, average depth of coverage and good SNP count. **Required options**