Add Beagle tool #3760
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Add Beagle tool #3760
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bgruening
approved these changes
Jun 26, 2021
tools/beagle/beagle.xml
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| help="It specifies a VCF file containing genotypes for the study samples. | ||
| Each VCF record must contain a GT (genotype) format field"/> | ||
| <section name="optional_inputs" title="Optional input files" expanded="true"> | ||
| <param argument="ref" type="data" format="vcf,binary" optional="true" label="Bref3 or VCF file with phased genotypes" |
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binary is bad, what is that? Do we need to add a new filetype?
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We can also just support VCF.
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I can try to include a new filetype; the binary format is bref3 https://faculty.washington.edu/browning/beagle/bref3.14May18.pdf.
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tools/beagle/beagle.xml
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| #end if | ||
| beagle | ||
| gt='${gt}' | ||
| #if $optional_inputs.ref and $optional_inputs.ref.ext == 'binary' |
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we do need to get rid of the binary here ... add a new filetype?
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bgruening
approved these changes
Jul 3, 2021
davebx
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Jul 8, 2021
* add_beagle * Fix boolean options * Fix tests * Fix test 1 * Include bref3 format and log output option * Include bref3 datatype * Fix tests
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FOR CONTRIBUTOR:
This tool was requested by a user in GHelp: original post.
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