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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| && mv output_dir/violin_atl.png '${output_violin_plot}' | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_reads" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz,bam,cram" multiple="true" label="Input reads" help="Long-read sequencing data in FASTA, FASTQ, BAM, or CRAM format (gzipped supported). Multiple files can be selected."/> |
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Please remove fastq and fastq.gz.
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
tools/telogator2/telogator2.xml
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| <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)"/> | ||
| <param name="random_seed" argument="--rng" type="integer" optional="true" label="Random seed" help="Random seed value for reproducibility (optional)"/> |
| </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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| <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.
| <when value="pbmm2"/> | ||
| </conditional> | ||
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| <param name="ref_fasta" type="data" format="fasta" optional="true" label="Reference FASTA for CRAM input" help="Required only if input is CRAM format"/> |
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Is there a connection to the custom reference?
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No, they are separate and could be pointing to different files!
Considering if I should update the wrapper and dropping support for cram files or do you believe that cram file is something that users? Since it's optional right now I guess the tool would fail if the user forget to set this optional parameter.
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
tools/telogator2/telogator2.xml
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| **Reference** | ||
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| Stephens, Z., & Kocher, J. P. (2024). Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC Bioinformatics, 25(1), 194. |
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This is already in the citation, or?
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True! I will remove the duplicated information
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