Mercurial > repos > anton > vcfcheck
annotate vcfcheck.xml @ 1:27478240ba22
Updated to vcflib 86723982aa
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 16:12:36 -0400 |
| parents | 42e3f0702878 |
| children | fb8033dcb750 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="vcfcheck" name="VCFcheck:" version="0.0.1"> |
| 2 <requirements> | |
|
1
27478240ba22
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Verify that the reference allele matches the reference genome</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 vcfcheck $failure_selector -f "${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="failure_selector" type="select" display="radio" label="Exclude or include failed sites"> | |
| 40 <option value="-x">Exculde failures (-x option)</option> | |
| 41 <option value="-k">Keep failures (-k option)</option> | |
| 42 </param> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="vcf" name="out_file1" /> | |
| 46 </outputs> | |
| 47 <stdio> | |
| 48 <regex match="index file" source="stderr" level="warning"/> | |
| 49 </stdio> | |
| 50 <tests> | |
| 51 <test> | |
| 52 <param name="reference_source_selector" value="history" /> | |
| 53 <param name="failure_selection" value="-x" /> | |
| 54 <param name="input_vcf" value="vcflib-phix.vcf"/> | |
| 55 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 56 <output name="out_file1" file="vcfcheck-test1.vcf"/> | |
| 57 </test> | |
| 58 </tests> | |
| 59 <help> | |
| 60 | |
| 61 Verifies that the VCF REF field matches the reference as described. | |
| 62 | |
| 63 The options are:: | |
| 64 | |
| 65 -x, --exclude-failures If a record fails, don't print it. Otherwise do. | |
| 66 -k, --keep-failures Print if the record fails, otherwise not. | |
| 67 | |
| 68 ---- | |
| 69 | |
| 70 Vcfcheck is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 71 | |
| 72 </help> | |
| 73 </tool> |