Mercurial > repos > iuc > telogator
changeset 0:afcb889cbce3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
| author | iuc |
|---|---|
| date | Thu, 04 Dec 2025 17:09:38 +0000 |
| parents | |
| children | |
| files | macros.xml telogator.xml telogator_make_ref.xml test-data/hg002-ont-1p.fa.gz test-data/hg002-ont-1p.sub.fa.gz test-data/hg002-telreads_pacbio.sub.fa.gz test-data/t2t_subset.fa.gz test-data/t2t_subset_with_telomeres.fa.gz |
| diffstat | 8 files changed, 573 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Dec 04 17:09:38 2025 +0000 @@ -0,0 +1,38 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">telogator2</requirement> + <requirement type="package" version="2.28">minimap2</requirement> + <requirement type="package" version="2.03">winnowmap</requirement> + <requirement type="package" version="1.13.1">pbmm2</requirement> + <yield/> + </requirements> + </xml> + <xml name="version_command"> + <version_command><![CDATA[telogator2 --version]]></version_command> + </xml> + <token name="@VERSION@">2.2.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.2</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0622</edam_topic> + <edam_topic>topic_0196</edam_topic> + <edam_topic>topic_3673</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3227</edam_operation> + <edam_operation>operation_3192</edam_operation> + </edam_operations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">telogator2</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12859-024-05807-5</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/telogator.xml Thu Dec 04 17:09:38 2025 +0000 @@ -0,0 +1,348 @@ +<tool id="telogator" name="Telogator" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>Measure allele-specific telomere length from long reads</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + #import re + + ## Create output directory + mkdir -p output_dir && + + ## Link input files with proper extensions since it's used to + ## define input types in telogator + #set $input_files = [] + #for $idx, $input_file in enumerate($input_reads) + #set $identifier = str($input_file.element_identifier) + #set $safe_name = re.sub('[^\w\-\.]', '_', $identifier) + ## Add extension only if filename doesn't already have appropriate extension + #if $input_file.is_of_type('fasta.gz') and not ($safe_name.endswith('.fa.gz') or $safe_name.endswith('.fasta.gz')) + #set $safe_name = $safe_name + '.fa.gz' + #elif $input_file.is_of_type('fasta') and not ($safe_name.endswith('.fa') or $safe_name.endswith('.fasta')) + #set $safe_name = $safe_name + '.fa' + #elif $input_file.is_of_type('fastqsanger.gz', 'fastq.gz') and not ($safe_name.endswith('.fq.gz') or $safe_name.endswith('.fastq.gz')) + #set $safe_name = $safe_name + '.fq.gz' + #elif $input_file.is_of_type('fastqsanger', 'fastq') and not ($safe_name.endswith('.fq') or $safe_name.endswith('.fastq')) + #set $safe_name = $safe_name + '.fq' + #elif $input_file.is_of_type('bam') and not $safe_name.endswith('.bam') + #set $safe_name = $safe_name + '.bam' + #elif $input_file.is_of_type('cram') and not $safe_name.endswith('.cram') + #set $safe_name = $safe_name + '.cram' + #end if + ln -sf '${input_file}' '${safe_name}' && + #silent $input_files.append($safe_name) + #end for + + ## Run telogator + telogator2 + -i #echo ' '.join($input_files) + -o output_dir + -r '${read_type}' + -p "\${GALAXY_SLOTS:-1}" + + ## Basic parameters + -l '${basic_params.min_read_length}' + -c '${basic_params.min_canonical_hits}' + -n '${basic_params.min_reads_cluster}' + -m '${basic_params.atl_method}' + #if str($basic_params.downsample) != '' + -d '${basic_params.downsample}' + #end if + #if str($basic_params.random_seed) != '' + --rng '${basic_params.random_seed}' + #end if + + ## Reference files + #if $reference_opts.custom_reference + -t '${reference_opts.custom_reference}' + #end if + #if $reference_opts.kmer_file + -k '${reference_opts.kmer_file}' + #end if + + ## Aligner selection + #if $aligner.aligner_choice == 'minimap2' + --minimap2 minimap2 + #elif $aligner.aligner_choice == 'winnowmap' + --winnowmap winnowmap + #if $aligner.winnowmap_k15 + --winnowmap-k15 '${aligner.winnowmap_k15}' + #end if + #elif $aligner.aligner_choice == 'pbmm2' + --pbmm2 pbmm2 + #end if + + ## Advanced filtering + --filt-tel '${advanced.filtering.filt_tel}' + --filt-nontel '${advanced.filtering.filt_nontel}' + --filt-sub '${advanced.filtering.filt_sub}' + --collapse-hom '${advanced.filtering.collapse_hom}' + + ${advanced.filtering.fast_aln} + + ## Hierarchical clustering parameters + -t0 '${advanced.clustering.t0}' + -t1 '${advanced.clustering.t1}' + -t2 '${advanced.clustering.t2}' + -tc '${advanced.clustering.tc}' + -ts '${advanced.clustering.ts}' + -th '${advanced.clustering.th}' + + ## Plot customization + -afa-x '${advanced.plotting.afa_x}' + -afa-t '${advanced.plotting.afa_t}' + -afa-a '${advanced.plotting.afa_a}' + -va-y '${advanced.plotting.va_y}' + -va-t '${advanced.plotting.va_t}' + -va-p '${advanced.plotting.va_p}' + + ## Move outputs to expected locations + && mv output_dir/tlens_by_allele.tsv '${output_tsv}' + && mv output_dir/all_final_alleles.png '${output_alleles_plot}' + && mv output_dir/violin_atl.png '${output_violin_plot}' + ]]></command> + <inputs> + <param name="input_reads" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,bam" multiple="true" label="Input reads" help="Long-read sequencing data in FASTA, FASTQ or BAM format. Multiple files can be selected."/> + + <param name="read_type" type="select" label="Read type" help="Sequencing platform type"> + <option value="ont">Oxford Nanopore (ONT)</option> + <option value="hifi" selected="true">PacBio HiFi</option> + </param> + + <section name="basic_params" title="Basic Parameters" expanded="true"> + <param name="min_read_length" argument="-l" type="integer" value="4000" min="0" label="Minimum read length" help="Minimum read length in base pairs"/> + <param name="min_canonical_hits" argument="-c" type="integer" value="8" min="0" label="Minimum canonical kmer hits" help="Minimum hits to tandem canonical kmer"/> + <param name="min_reads_cluster" argument="-n" type="integer" value="3" min="1" label="Minimum reads per cluster" help="Minimum number of reads required per cluster. Recommended: PacBio Revio HiFi (30x): 4, PacBio Sequel II (10x): 3, Nanopore R10 (30x): 4"/> + <param name="atl_method" argument="-m" type="select" label="ATL calculation method" help="Method for calculating allele-specific telomere length"> + <option value="p75" selected="true">75th percentile (p75)</option> + <option value="mean">Mean</option> + <option value="median">Median</option> + <option value="max">Maximum</option> + </param> + <param name="downsample" argument="-d" type="integer" optional="true" value="" label="Downsample telomere reads" help="Downsample to N telomere reads (optional)"/> + <param name="random_seed" argument="--rng" type="integer" optional="true" value="" label="Random seed" help="Random seed value for reproducibility (optional)"/> + </section> + + <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="tsv" optional="true" label="Telomere kmers file" help="Optional telomere k-mers file. If omitted, a built-in human telomere k-mers file is used."/> + </section> + + <conditional name="aligner"> + <param name="aligner_choice" type="select" label="Alignment tool" help="Select which aligner to use"> + <option value="minimap2" selected="true">minimap2</option> + <option value="winnowmap">winnowmap</option> + <option value="pbmm2">pbmm2</option> + </param> + <when value="minimap2"/> + <when value="winnowmap"> + <param argument="--winnowmap-k15" type="data" format="txt" optional="true" label="Winnowmap k15 file" help="High-frequency kmers file for winnowmap"/> + </when> + <when value="pbmm2"/> + </conditional> + + <section name="advanced" title="Advanced Parameters" expanded="false"> + <section name="filtering" title="Filtering Thresholds" expanded="true"> + <param argument="--filt-tel" type="integer" value="400" min="0" label="Minimum terminating telomere" help="Minimum terminating telomere length in bp"/> + <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="--fast-aln" falsevalue="" checked="false" label="Use fast alignment" help="Use faster but less accurate pairwise alignment"/> + </section> + + <section name="clustering" title="Hierarchical Clustering (TREECUT) Parameters" expanded="false"> + <param argument="-t0" type="float" value="0.200" min="0" max="1" label="TVR clustering iteration 0" help="Threshold for TVR clustering in iteration 0"/> + <param argument="-t1" type="float" value="0.150" min="0" max="1" label="TVR clustering iteration 1" help="Threshold for TVR clustering in iteration 1"/> + <param argument="-t2" type="float" value="0.100" min="0" max="1" label="TVR clustering iteration 2" help="Threshold for TVR clustering in iteration 2"/> + <param argument="-tc" type="float" value="0.050" min="0" max="1" label="TVR clustering collapse" help="Threshold for collapsing TVR clusters"/> + <param argument="-ts" type="float" value="0.200" min="0" max="1" label="Subtel cluster refinement" help="Threshold for subtelomere cluster refinement"/> + <param argument="-th" type="float" value="0.050" min="0" max="1" label="Collapsing aligned alleles" help="Threshold for collapsing aligned alleles"/> + </section> + + <section name="plotting" title="Plot Customization" expanded="false"> + <param argument="-afa-x" type="integer" value="15000" min="0" label="All alleles plot X-axis max" help="Maximum X-axis value for all final alleles plot"/> + <param argument="-afa-t" type="integer" value="1000" min="0" label="All alleles plot tick steps" help="Tick step size for all final alleles plot"/> + <param argument="-afa-a" type="integer" value="100" min="0" label="Minimum ATL for plot inclusion" help="Minimum allele-specific telomere length for inclusion in all final alleles plot"/> + <param argument="-va-y" type="integer" value="20000" min="0" label="Violin plot Y-axis max" help="Maximum Y-axis value for violin plot"/> + <param argument="-va-t" type="integer" value="5000" min="0" label="Violin plot tick steps" help="Tick step size for violin plot"/> + <param argument="-va-p" type="integer" value="2" min="1" label="Ploidy" help="Number of alleles per chromosome arm (ploidy)"/> + </section> + </section> + </inputs> + <outputs> + <data name="output_tsv" format="tabular" label="${tool.name} on ${on_string}: Telomere lengths by allele"/> + <data name="output_alleles_plot" format="png" label="${tool.name} on ${on_string}: All final alleles plot"/> + <data name="output_violin_plot" format="png" label="${tool.name} on ${on_string}: Violin plot"/> + </outputs> + <tests> + <!-- Test 1: PacBio HiFi data --> + <test expect_num_outputs="3"> + <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> + <param name="read_type" value="hifi"/> + <conditional name="aligner"> + <param name="aligner_choice" value="minimap2"/> + </conditional> + <output name="output_tsv"> + <assert_contents> + <has_text text="chr"/> + <has_text text="position"/> + <has_text text="allele_id"/> + <has_text text="TL_p75"/> + <has_n_columns n="11"/> + <has_n_lines n="13" delta="2"/> + <has_line_matching expression="chr\d+[pq]\t\d+.*"/> + </assert_contents> + </output> + <output name="output_alleles_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + <output name="output_violin_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + </test> + <!-- Test 2: Oxford Nanopore data, 2 inputs --> + <test expect_num_outputs="3"> + <param name="input_reads" value="hg002-ont-1p.fa.gz,hg002-ont-1p.sub.fa.gz"/> + <param name="read_type" value="ont"/> + <conditional name="aligner"> + <param name="aligner_choice" value="minimap2"/> + </conditional> + <output name="output_tsv"> + <assert_contents> + <has_text text="chr"/> + <has_text text="position"/> + <has_text text="allele_id"/> + <has_text text="TL_p75"/> + <has_n_columns n="11"/> + <has_n_lines n="2" delta="10"/> + </assert_contents> + </output> + <output name="output_alleles_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + <output name="output_violin_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + </test> + <!-- Test 3: PacBio HiFi data, pbmm2 --> + <test expect_num_outputs="3"> + <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> + <param name="read_type" value="hifi"/> + <conditional name="aligner"> + <param name="aligner_choice" value="pbmm2"/> + </conditional> + <output name="output_tsv"> + <assert_contents> + <has_text text="chr"/> + <has_text text="position"/> + <has_text text="allele_id"/> + <has_text text="TL_p75"/> + <has_n_columns n="11"/> + <has_n_lines n="13" delta="2"/> + </assert_contents> + </output> + <output name="output_alleles_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + <output name="output_violin_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + </test> + <!-- Test 4: PacBio HiFi data, winnowmap --> + <test expect_num_outputs="3"> + <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> + <param name="read_type" value="hifi"/> + <conditional name="aligner"> + <param name="aligner_choice" value="winnowmap"/> + </conditional> + <output name="output_tsv"> + <assert_contents> + <has_text text="chr"/> + <has_text text="position"/> + <has_text text="allele_id"/> + <has_text text="TL_p75"/> + <has_n_columns n="11"/> + <has_n_lines n="13" delta="2"/> + </assert_contents> + </output> + <output name="output_alleles_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + <output name="output_violin_plot"> + <assert_contents> + <has_size min="10000" max="500000"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Telogator2 measures allele-specific telomere length (ATL) and characterizes telomere variant repeat (TVR) sequences from long-read sequencing data (PacBio HiFi or Oxford Nanopore). + +The tool performs the following analyses: + +1. Extracts reads containing telomeric sequences +2. Aligns reads to reference genome to identify chromosome arms +3. Clusters reads by TVR sequences to identify individual alleles +4. Calculates allele-specific telomere lengths +5. Generates visualizations of telomere length distributions + +**Inputs** + +- Long-read sequencing data (FASTA, FASTQ, BAM, or CRAM format) +- Optional custom reference genome and kmer files +- Platform-specific parameters (PacBio HiFi or Oxford Nanopore) + +**Outputs** + +1. **tlens_by_allele.tsv**: Primary results table containing: + + - chr: Chromosome arm (or chrU for unmapped) + - position: Anchor coordinate + - ref_samp: Reference contig alignment + - allele_id: Allele identifier (suffix 'i' indicates interstitial telomeric regions) + - TL_p75: Allele-specific telomere length (75th percentile by default) + - read_TLs, read_lengths, read_mapq: Per-read metrics + - tvr_len, tvr_consensus: Telomere variant repeat characteristics + - supporting_reads: Read identifiers + +2. **all_final_alleles.png**: Visualization of all identified alleles + +3. **violin_atl.png**: Violin plot showing ATL distributions by chromosome arm + +**Platform-Specific Recommendations** + +- **PacBio Revio HiFi (30x coverage)**: Set minimum reads per cluster to 4 +- **PacBio Sequel II (10x coverage)**: Set minimum reads per cluster to 3 +- **Nanopore R10 (30x coverage)**: Set minimum reads per cluster to 4 +- **Large enrichment datasets**: Increase minimum reads per cluster to 10 + +**Important Notes** + +- For PacBio Revio data, include both "hifi" and "fail" BAM files +- Older Nanopore data (Guppy basecalled) may have high error rates in telomere regions +- Runtime improves with additional CPU cores (increase processes parameter) +- Alleles with suffix 'i' are interstitial telomeric regions and may need to be excluded from downstream analysis + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/telogator_make_ref.xml Thu Dec 04 17:09:38 2025 +0000 @@ -0,0 +1,187 @@ +<tool id="telogator_make_ref" name="Telogator Make Reference" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>Create custom telogator reference from a T2T assembly</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + #import re + #set $identifier = str($input_fasta.element_identifier) + #set $safe_name = re.sub('[^\w\-\.]', '_', $identifier) + #if $input_fasta.is_of_type('fasta.gz') and not ($safe_name.endswith('.fa.gz') or $safe_name.endswith('.fasta.gz')) + #set $safe_name = $safe_name + '.fa.gz' + #elif $input_fasta.is_of_type('fasta') and not ($safe_name.endswith('.fa') or $safe_name.endswith('.fasta')) + #set $safe_name = $safe_name + '.fa' + #end if + mkdir -p output_dir && + ln -sf '${input_fasta}' '${safe_name}' && + make_telogator_ref + -i '${safe_name}' + -o output_dir/output_ref.fa + -s '${sample_name}' + -c '${contig_list}' + ## Optional kmer file + #if $kmer_file + -k '${kmer_file}' + #end if + ## Minimum telomere length + -m '${min_tel_length}' + ## Optional flags + ${add_tel} + ${plot} + ## Move outputs + && mv output_dir/output_ref.fa '${output_fasta}' + ]]></command> + <inputs> + <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Input T2T reference FASTA" help="Telomere-to-telomere reference genome assembly in FASTA format (gzipped supported)"/> + <param name="sample_name" argument="-s" type="text" value="sample" label="Sample name" help="Sample name to prepend to contig identifiers in the output"> + <validator type="regex" message="Sample name must contain only alphanumeric characters and hyphens">^[a-zA-Z0-9-]+$</validator> + </param> + <param name="contig_list" argument="-c" type="text" value="chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" label="List of contigs" help="Comma-delimited list of contigs to include. Default is all human chromosomes."> + <validator type="empty_field"/> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="kmer_file" argument="-k" type="data" format="tsv" optional="true" value="" label="Telomere kmers file" help="Optional telomere k-mers file. If omitted, a built-in human telomere k-mers file is used."/> + <param name="min_tel_length" argument="-m" type="integer" value="0" min="0" label="Minimum telomere length" help="Minimum telomere length required at contig ends (in base pairs)"/> + <param name="add_tel" type="boolean" truevalue="--add-tel" falsevalue="" checked="false" label="Include masked telomeres" help="Include masked telomeres as separate contigs in the output"/> + <param name="plot" type="boolean" truevalue="--plot" falsevalue="" checked="false" label="Generate telomere signal plots" help="Generate PNG plots showing telomere signals for each chromosome arm"/> + </inputs> + <outputs> + <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: Reference FASTA"/> + <collection name="plots" type="list" label="${tool.name} on ${on_string}: Telomere signal plots"> + <discover_datasets pattern="(?P<designation>.+)\.png$" directory="output_dir" format="png"/> + <filter>plot</filter> + </collection> + </outputs> + <tests> + <!-- Test 1: Basic usage with minimal parameters --> + <test expect_num_outputs="1"> + <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz"/> + <param name="sample_name" value="test-sample1"/> + <param name="contig_list" value="t2t-i002c-mat_chr11p,t2t-i002c-mat_chr11q,t2t-i002c-mat_chr12p,t2t-i002c-mat_chr12q,t2t-i002c-mat_chr13p,t2t-i002c-mat_chr13q"/> + <output name="output_fasta"> + <assert_contents> + <has_text text=">test-sample"/> + <has_line_matching expression="^>.*"/> + <has_line_matching expression="^[ACGTN]+$"/> + <has_size value="6100428" delta="100000"/> + <not_has_text text=">test-sample1_tel-"/> + </assert_contents> + </output> + </test> + <!-- Test 2: With plot generation --> + <test expect_num_outputs="2"> + <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz"/> + <param name="sample_name" value="test-sample2"/> + <param name="plot" value="true"/> + <param name="contig_list" value="t2t-i002c-mat_chr11p,t2t-i002c-mat_chr11q,t2t-i002c-mat_chr12p,t2t-i002c-mat_chr12q,t2t-i002c-mat_chr13p,t2t-i002c-mat_chr13q"/> + <output name="output_fasta"> + <assert_contents> + <has_text text=">test-sample2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list"> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr11pp"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr11qq"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr12pp"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr12qq"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr13pp"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + <element name="test-sample2_telsignal_t2t-i002c-mat_chr13qq"> + <assert_contents> + <has_size min="10000"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- Test 3: use telomere parameters --> + <test expect_num_outputs="1"> + <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz" /> + <param name="sample_name" value="test-sample3"/> + <param name="min_tel_length" value="1000"/> + <param name="add_tel" value="true"/> + <param name="contig_list" value="t2t-i002c-mat_chr11p,t2t-i002c-mat_chr11q,t2t-i002c-mat_chr12p,t2t-i002c-mat_chr12q,t2t-i002c-mat_chr13p,t2t-i002c-mat_chr13q"/> + <output name="output_fasta"> + <assert_contents> + <has_text text=">test-sample3"/> + <has_line_matching expression="^>.*"/> + <has_line_matching expression="^[ACGTN]+$"/> + <has_size value="4066952" delta="100000"/> + <has_text text=">test-sample3_tel-"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Telogator Make Reference creates a custom telogator reference database from a telomere-to-telomere (T2T) reference genome assembly. This tool is essential for analyzing telomeres in non-human organisms or custom genome assemblies. + +The tool performs the following steps: + +1. Reads the input T2T reference FASTA file +2. Identifies telomeric sequences at contig ends +3. Optionally filters and remaps contigs +4. Creates a processed reference suitable for telogator analysis +5. Generates an index file (.fai) for the reference +6. Optionally generates visualization plots of telomere signals + +**When to use this tool** + +Use this tool when you need to: + +- Analyze telomeres in non-human organisms (e.g., mouse, maize, other species) +- Work with custom or newly assembled T2T genomes +- Create a reference from alternative human T2T assemblies (T2T-yao, T2T-cn1, etc.) +- Prepare references with specific contig selections or naming conventions + +**Inputs** + +- **T2T reference FASTA**: A telomere-to-telomere reference genome assembly +- **Sample name**: Identifier prepended to contig names (use organism/assembly name) +- **Contig list**: Comma-delimited list of contigs to include (defaults to all human chromosomes) +- **Telomere kmers file** (optional): Custom telomere repeat patterns for non-human organisms +- **Minimum telomere length**: Filter contigs by minimum telomere length at ends + +**Outputs** + +1. **Reference FASTA**: Processed telogator reference file ready for use with telogator +2. **Reference index (.fai)**: Index file for the created reference FASTA +3. **Telomere signal plots** (optional): PNG plots showing telomere signals for each chromosome arm + +**Important Notes** + +- The input FASTA should be a high-quality T2T assembly with telomeres at contig ends +- The sample name should be descriptive (e.g., organism name, assembly version), may not contain underscores +- The contig list defaults to human chromosomes; modify it for other organisms or custom assemblies +- For non-human organisms, provide a telomere kmers file matching the species' telomere repeats + + ]]></help> + <expand macro="citations"/> +</tool>