Mercurial > repos > anton > vcfprimers
annotate vcfprimers.xml @ 2:47dd84123b42
Updated tool version to 0.0.2
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 16:50:33 -0400 |
| parents | 8be427d0e4c3 |
| children | f3243301d74f |
| rev | line source |
|---|---|
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2
47dd84123b42
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
1
diff
changeset
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1 <tool id="vcfprimers" name="VCFprimers:" version="0.0.2"> |
| 0 | 2 <requirements> |
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1
8be427d0e4c3
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
|
3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> |
| 5 </requirements> | |
| 6 <description>Extract flanking sequences for each VCF record</description> | |
| 7 <command> | |
| 8 #set $reference_fasta_filename = "localref.fa" | |
| 9 #if str( $reference_source.reference_source_selector ) == "history": | |
| 10 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 11 #else: | |
| 12 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 13 #end if | |
| 14 vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command> | |
| 15 <inputs> | |
| 16 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" /> | |
| 17 <conditional name="reference_source"> | |
| 18 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
| 19 <option value="cached">Locally cached</option> | |
| 20 <option value="history">History</option> | |
| 21 </param> | |
| 22 <when value="cached"> | |
| 23 <param name="ref_file" type="select" label="Select reference genome"> | |
| 24 <options from_data_table="fasta_indexes"> | |
| 25 </options> | |
| 26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 27 </param> | |
| 28 </when> | |
| 29 <when value="history"> <!-- FIX ME!!!! --> | |
| 30 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 31 </when> | |
| 32 </conditional> | |
| 33 <param name="primer_length" type="integer" value="20" label="The length of the primer sequences on each side of the variant" help="default = 20 bp" /> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="fasta" name="out_file1" /> | |
| 37 </outputs> | |
| 38 <stdio> | |
| 39 <exit_code range="1:" level="fatal" /> | |
| 40 </stdio> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="reference_source_selector" value="history" /> | |
| 44 <param name="input_vcf" value="vcflib-phix.vcf"/> | |
| 45 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 46 <param name="primer_length" value="5" /> | |
| 47 <output name="out_file1" file="vcfprimers-test1.fasta"/> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 51 | |
| 52 For each VCF record, extract the flanking sequences, and write them to stdout as FASTA | |
| 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 | |
| 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, | |
| 57 for example:: | |
| 58 | |
| 59 >20_233255_LEFT | |
| 60 CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA | |
| 61 >20_233255_RIGHT | |
| 62 ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA | |
| 63 | |
| 64 ---- | |
| 65 | |
| 66 Vcfprimers is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 67 | |
| 68 </help> | |
| 69 </tool> |