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1 <tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0">
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2 <description>from VCF data</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 grep "#CHROM" '$input_vcf' > test.head &&
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5 tr '\t' '\n' < test.head > samples.txt &&
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6 sed -i 1,9d samples.txt &&
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7 awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output'
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8 ]]></command>
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9 <inputs>
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10 <param name="input_vcf" type="data" format="vcf" label="VCF file"/>
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="tabular"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input_vcf" value="input.vcf" ftype="vcf"/>
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18 <output name="output" file="output.tabular" ftype="tabular"/>
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19 </test>
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20 </tests>
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21 <help>
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22 **What it does**
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23
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24 Extracts information from a VCF file that contains Affymetrix identifiers and produces a file that contains
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25 a subset of the identifiers combined with additional data to generate the genotype population information
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26 for use as input to the Corals Multilocus Genotype tool. This tool must be able to access the corals (stag)
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27 database.
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28 </help>
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29 <citations>
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30 <citation type="bibtex">
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31 @misc{None,
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32 journal = {None},
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33 author = {Baums I},
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34 title = {Manuscript in preparation},
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35 year = {None},
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36 url = {http://baumslab.org}
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37 </citation>
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38 </citations>
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39 </tool>
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