Mercurial > repos > brigidar > vcf_to_snp
changeset 3:a928631d8297 draft
new wrapper
author | brigidar |
---|---|
date | Mon, 02 Nov 2015 19:31:03 -0500 |
parents | ea2f686dfd4a |
children | 866cd9ce1cbd |
files | vcf_to_snp.xml |
diffstat | 1 files changed, 3 insertions(+), 7 deletions(-) [+] |
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--- a/vcf_to_snp.xml Mon Nov 02 19:30:43 2015 -0500 +++ b/vcf_to_snp.xml Mon Nov 02 19:31:03 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vcf_snp" name="vcf to snp" version="0.1"> +<tool id="vcf_snp" name="vcf to snp" version="0.2"> <description>vcf to snp for fasta</description> <requirements> <!-- Should just use the filter snp that's installed in the path --> @@ -12,11 +12,7 @@ <command interpreter="python"> vcf_snp.py -s ${vcf} - -o output.txt; - cut -f1 output.txt > header.txt | cut -f2- output.txt > seq.txt; - cat seq.txt | sed 's/[[:blank:]]//g' >seq2.txt; - paste header.txt seq2.txt >tab.txt; - + -o output.txt </command> @@ -40,7 +36,7 @@ **What it does** -Transforms a vcf into a snp tab file +Transforms a vcf into a snp tab file. Has to take the nucleotide from the reference column when identical. -------------