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Commit message:
Uploaded |
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modified:
filter_vcf.xml |
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| diff -r e2ee6acf8752 -r 74f595df6e51 filter_vcf.xml --- a/filter_vcf.xml Thu Jun 16 06:39:37 2016 -0400 +++ b/filter_vcf.xml Thu Jun 16 06:39:51 2016 -0400 |
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| @@ -19,6 +19,7 @@ filter_vcf.sh $output $input + $ref_fa #if str($onlygood) == "false": onlygood #else @@ -36,6 +37,8 @@ <inputs> <param name="input" type="data" format="vcf" label="VCF File to filter" /> + <param name="ref_fa" type="data" format="fasta" label="Reference genome fasta file" help="REQUIRED."/> + <repeat name="snp_filter" title="SNP Filter" help=""> <conditional name="snp_filter_type"> <param name="snp_filter_type_selector" type="select" label="SNP Filter Type"> @@ -108,5 +111,9 @@ \-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written. +\-\-reference REFERENCE, -r REFERENCE mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF. + +\-\-only-good Write only variants that PASS all filters (default all variants are written). + </help> </tool> |