Mercurial > repos > anton > vcfgeno2haplo
annotate vcfgeno2haplo.xml @ 1:fee06b54bdd9
Updated to vcflib 86723982aa
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 16:14:58 -0400 |
| parents | e19406b6e652 |
| children | a6cd013745fd |
| rev | line source |
|---|---|
| 0 | 1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.1"> |
| 2 <requirements> | |
|
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fee06b54bdd9
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
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diff
changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Convert genotype-based phased alleles into haplotype alleles</description> | |
| 6 <command> | |
| 7 #set $reference_fasta_filename = "localref.fa" | |
| 8 #if str( $reference_source.reference_source_selector ) == "history": | |
| 9 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 10 #else: | |
| 11 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 12 #end if | |
| 13 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> | |
| 14 <inputs> | |
| 15 <conditional name="reference_source"> | |
| 16 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
| 17 <option value="cached">Locally cached</option> | |
| 18 <option value="history">History</option> | |
| 19 </param> | |
| 20 <when value="cached"> | |
| 21 <param name="ref_file" type="select" label="Select reference genome"> | |
| 22 <options from_data_table="fasta_indexes"> | |
| 23 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | |
| 24 </options> | |
| 25 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 26 </param> | |
| 27 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset"> | |
| 28 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future | |
| 29 <validator type="unspecified_build" /> | |
| 30 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> | |
| 31 --> | |
| 32 </param> | |
| 33 </when> | |
| 34 <when value="history"> <!-- FIX ME!!!! --> | |
| 35 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 36 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> | |
| 37 </when> | |
| 38 </conditional> | |
| 39 <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" /> | |
| 40 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" /> | |
| 41 <!-- <option value=" ">Output entire haplotype</option> | |
| 42 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by ":")</option> | |
| 43 </param> --> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <data format="vcf" name="out_file1" /> | |
| 47 </outputs> | |
| 48 <stdio> | |
| 49 <exit_code range="1:" level="fatal" /> | |
| 50 </stdio> | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="reference_source_selector" value="history" /> | |
| 54 <param name="output_option" value="true" /> | |
| 55 <param name="window_size" value="5000" /> | |
| 56 <param name="input_vcf" value="vcflib-phix.vcf"/> | |
| 57 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 58 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/> | |
| 59 </test> | |
| 60 </tests> | |
| 61 <help> | |
| 62 | |
| 63 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input. | |
| 64 | |
| 65 The options are:: | |
| 66 | |
| 67 -r, --reference FILE FASTA reference file, required with -i and -u | |
| 68 -w, --window-size N Merge variants at most this many bp apart (default 30) | |
| 69 -o, --only-variants Don't output the entire haplotype, just concatenate | |
| 70 REF/ALT strings (delimited by ":") | |
| 71 | |
| 72 ---- | |
| 73 | |
| 74 Vcfgeno2haplo is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 75 | |
| 76 </help> | |
| 77 </tool> |