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1 <tool id="vcf_expression_annotator" name="VCF Expression Annotator" version="1.0">
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2 <command>vcf-expression-annotator ${input_vcf} ${input_expression} ${expression_method} ${gene_or_transcript} -o $output</command>
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3 <inputs>
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4 <param name="input_vcf" type="data" format="vcf" label="Input VCF" />
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5 <param name="input_expression" type="data" label="Input expression data" />
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6 <param name="expression_method" type="select" label="expression_method">
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7 <option value="kallisto">Kallisto</option>
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8 <option value="stringtie">Stringtie</option>
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9 <option value="cufflinks">Cufflinks</option>
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10 </param>
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11 <param name="gene_or_transcript" type="select" label="Gene or Transcript">
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12 <option value="gene">Gene</option>
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13 <option value="Transcript">Transcript</option>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="vcf" name="output" />
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18 </outputs>
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19 <help>
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20
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21 </help>
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22 </tool> |
