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1 <?xml version="1.0"?>
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2
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3 <tool id="hgvs2vcf_1" name="Convert a variant table with HGVS syntax into a VCF">
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4 <version_string>echo 1.0.0</version_string>
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5 <command interpreter="perl">hgvs_to_vcf $in_hgvs_table $output_vcf $sample_name hg19
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6 </command>
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7 <inputs>
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8 <param name="in_hgvs_table" format="achri_snp_table" type="data" label="SNP table with HGVS calls"/>
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9 <param type="text" name="sample_name" value="ANON" label="Name for the sample in the output VCF file's header"/>
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10 </inputs>
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11 <outputs>
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12 <data format="vcf" name="output_vcf" type="data" label="Sequence variant calls"/>
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13 </outputs>
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14
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15 <tests>
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16 </tests>
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17
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18 <help>This tools converts the tabular format used to describe variants and associate annotation at ACHRI into a standard Variant Calls Format (VCF) version 4.1 file, which is accepted by many genetic analysis programs.</help>
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19 </tool>
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