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comparison vcfprimers.xml @ 3:f3243301d74f draft default tip

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author anton
date Mon, 15 Sep 2014 14:53:14 -0400
parents 47dd84123b42
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2:47dd84123b42 3:f3243301d74f
1 <tool id="vcfprimers" name="VCFprimers:" version="0.0.2"> 1 <tool id="vcfprimers" name="VCFprimers:" version="0.0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="86723982aa">vcflib</requirement> 3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
5 </requirements> 5 </requirements>
6 <description>Extract flanking sequences for each VCF record</description> 6 <description>Extract flanking sequences for each VCF record</description>
7 <command> 7 <command>
8 #set $reference_fasta_filename = "localref.fa" 8 #set $reference_fasta_filename = "localref.fa"
47 <output name="out_file1" file="vcfprimers-test1.fasta"/> 47 <output name="out_file1" file="vcfprimers-test1.fasta"/>
48 </test> 48 </test>
49 </tests> 49 </tests>
50 <help> 50 <help>
51 51
52 For each VCF record, extract the flanking sequences, and write them to stdout as FASTA 52 For each VCF record, extract the flanking sequences, and write them as FASTA
53 records suitable for alignment. This tool is intended for use in designing validation 53 records suitable for alignment. This tool is intended for use in designing validation
54 experiments. Primers extracted which would flank all of the alleles at multi-allelic 54 experiments. Primers extracted which would flank all of the alleles at multi-allelic
55 sites. The name of the FASTA "reads" indicates the VCF record which they apply to. 55 sites. The name of the FASTA "reads" indicates the VCF record which they apply to.
56 The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer, 56 The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
57 for example:: 57 for example::