Mercurial > repos > iuc > ucsc_fatovcf
changeset 2:3c19c84fbce2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf commit 303002db06287fb25306020c4391626842f52162
| author | iuc |
|---|---|
| date | Sun, 22 Sep 2024 07:26:30 +0000 |
| parents | d9965e143053 |
| children | |
| files | fatovcf.xml |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/fatovcf.xml Thu Sep 21 13:12:43 2023 +0000 +++ b/fatovcf.xml Sun Sep 22 07:26:30 2024 +0000 @@ -48,7 +48,7 @@ ]]></command> <inputs> <param name="in_fasta" format="fasta" type="data" label="FASTA Alignment" help="Must contain a series of sequences with different names and the same length. Both N and - are treated as missing information." /> - + <conditional name="ref_seq"> <param name="refSeq" type="select" label="Determine reference sequence" help="Which sequence from the FASTA file should be used as the reference sequence."> <option value="" selected="true">Use the first sequence as reference</option> @@ -76,7 +76,7 @@ <param argument="-windowSize" type="integer" min="0" value="0" label="Window size to mask bases" help="Mask any base for which there are at least -minAmbigWindow bases in a window of +-N bases around the base. Masking approach adapted from https://github.com/roblanf/sarscov2phylo/blob/master/scripts/mask_seq.py Use -windowSize=7 for same results. Default: 0" /> <param argument="-minAmbigInWindow" type="integer" min="1" value="2" label="Minimum of ambiguous characters within the window given above" help="When -windowSize is provided, mask any base for which there are at least this many N, ambiguous or gap characters within the window. Default: 2" /> </section> - + <param argument="-includeNoAltN" type="boolean" truevalue="-includeNoAltN" falsevalue="" label="Include positions without defined ALT allele" help="Include base positions with no alternate alleles observed, but at least one N (missing base/no-call). Default: false" /> <param argument="-minAc" type="integer" min="0" value="0" label="Minimum allele count" help="Ignore alternate alleles observed fewer than N times. Default: 0" /> <param argument="-minAf" type="float" min="0.0" max="1.0" value="0.0" label="Minimum allele frequency" help="Ignore alternate alleles observed in less than F of non-N bases. Default: 0.0" /> @@ -136,7 +136,11 @@ `faToVcf`_ is a tool to extract a VCF from a multi-sequence FASTA alignment. -.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +For implementation details see faToVcf's `source code`_. + +.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/faToVcf/faToVcf.c + ]]> </help> <citations> <citation type="doi">10.1093/bib/bbs038</citation>