Mercurial > repos > greg > vsnp_statistics

changeset 2:7fe0cbb8c894 draft

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Uploaded
author greg
date Thu, 30 Apr 2020 10:26:20 -0400
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**