add wrapper for telogator2 #7481
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will stay in draft mode until I can add the tool for building reference files |
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tools/telogator2/telogator2.xml
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| <option value="median">Median</option> | ||
| <option value="max">Maximum</option> | ||
| </param> | ||
| <param name="downsample" argument="-d" type="integer" optional="true" label="Downsample telomere reads" help="Downsample to N telomere reads (optional)"/> |
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I remember that we need value="" for optional parameters
| </section> | ||
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| <section name="reference_opts" title="Reference Options" expanded="false"> | ||
| <param name="custom_reference" argument="-t" type="data" format="fasta" optional="true" label="Custom reference FASTA" help="Optional custom telogator reference FASTA file. If not provided, built-in human T2T reference will be used."/> |
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human T2T
Is this in the container?
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yes! A default human T2T (also maze and mouse) reference is included. I'm also adding the reference building tool, should be in bioconda this week.
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Would it maybe be wise to require the user to provide a reference and not rely on the once included? Right now you loose a bit of the data tracabillity since the included references are include in the source package, and it's not super clear which reference version that have been used to build the included ones.
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Reproducibility is given IMO. Only transparency is questionable. Maybe also ask upstream?
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| <section name="reference_opts" title="Reference Options" expanded="false"> | ||
| <param name="custom_reference" argument="-t" type="data" format="fasta" optional="true" label="Custom reference FASTA" help="Optional custom telogator reference FASTA file. If not provided, built-in human T2T reference will be used."/> | ||
| <param name="kmer_file" argument="-k" type="data" format="txt" optional="true" label="Telomere kmers file" help="Optional telomere kmers file (required for non-human organisms like mouse or maize)"/> |
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Any more info in this?
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Information about the kmer file is currently very sparse on in the repo. I have asked them to add more information about it.
tools/telogator2/telogator2.xml
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| <param argument="--filt-nontel" type="integer" value="100" min="0" label="Maximum terminating non-telomere" help="Maximum terminating non-telomere length in bp"/> | ||
| <param argument="--filt-sub" type="integer" value="1000" min="0" label="Minimum terminating subtelomere" help="Minimum terminating subtelomere length in bp"/> | ||
| <param argument="--collapse-hom" type="integer" value="1000" min="0" label="Collapse homologous alleles" help="Merge alleles within this distance in bp"/> | ||
| <param argument="--fast-aln" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use fast alignment" help="Use faster but less accurate pairwise alignment"/> |
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Use truevalue="--fast-aln" falsevalue="" then you can just $fast_aln in the command section and don't need the if statement
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