comparison vcfprimers.xml @ 3:f3243301d74f draft default tip

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2:47dd84123b42

<tool id="vcfprimers" name="VCFprimers:" version="0.0.2">
<requirements>
    <requirement type="package" version="86723982aa">vcflib</requirement>
    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
</requirements>
  <description>Extract flanking sequences for each VCF record</description>
  <command>
    #set $reference_fasta_filename = "localref.fa"

      <output name="out_file1" file="vcfprimers-test1.fasta"/>
    </test>
    </tests>
  <help>

For each VCF record, extract the flanking sequences, and write them to stdout as FASTA
records suitable for alignment.  This tool is intended for use in designing validation
experiments.  Primers extracted which would flank all of the alleles at multi-allelic
sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
for example::

3:f3243301d74f

<tool id="vcfprimers" name="VCFprimers:" version="0.0.2">
<requirements>
    <requirement type="package" version="8a5602bf07">vcflib</requirement>
    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
</requirements>
  <description>Extract flanking sequences for each VCF record</description>
  <command>
    #set $reference_fasta_filename = "localref.fa"

      <output name="out_file1" file="vcfprimers-test1.fasta"/>
    </test>
    </tests>
  <help>

For each VCF record, extract the flanking sequences, and write them as FASTA
records suitable for alignment.  This tool is intended for use in designing validation
experiments.  Primers extracted which would flank all of the alleles at multi-allelic
sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
for example::