| Previous changeset 2:ea2f686dfd4a (2015-11-02) Next changeset 4:866cd9ce1cbd (2015-11-02) |
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Commit message:
new wrapper |
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modified:
vcf_to_snp.xml |
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| diff -r ea2f686dfd4a -r a928631d8297 vcf_to_snp.xml --- 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 |
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| @@ -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. ------------- |