view affy_ids_for_genotyping.xml @ 2:b9e110cbba99 draft

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<tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0">
    <description>from VCF data</description>
    <command detect_errors="exit_code"><![CDATA[
grep "#CHROM" '$input_vcf' > test.head &&
tr '\t' '\n' < test.head > samples.txt &&
sed -i 1,9d samples.txt &&
awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output'
]]></command>
    <inputs>
        <param name="input_vcf" type="data" format="vcf" label="VCF file"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_vcf" value="input.vcf" ftype="vcf"/>
            <output name="output" file="output.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
**What it does**

Extracts information from a VCF file that contains Affymetrix identifiers and produces a file that contains
a subset of the identifiers combined with additional data to generate the genotype population information
for use as input to the Corals Multilocus Genotype tool.  This tool must be able to access the corals (stag)
database.
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation>
    </citations>
</tool>