Mercurial > repos > iuc > telogator
annotate telogator.xml @ 0:afcb889cbce3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
| author | iuc |
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| date | Thu, 04 Dec 2025 17:09:38 +0000 |
| parents | |
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| rev | line source |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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changeset
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1 <tool id="telogator" name="Telogator" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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2 <description>Measure allele-specific telomere length from long reads</description> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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3 <macros> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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changeset
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4 <import>macros.xml</import> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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5 </macros> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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6 <expand macro="edam_ontology"/> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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7 <expand macro="xrefs"/> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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8 <expand macro="requirements"/> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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9 <expand macro="version_command"/> |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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11 #import re |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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12 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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13 ## Create output directory |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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14 mkdir -p output_dir && |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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diff
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15 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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16 ## Link input files with proper extensions since it's used to |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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17 ## define input types in telogator |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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18 #set $input_files = [] |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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19 #for $idx, $input_file in enumerate($input_reads) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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20 #set $identifier = str($input_file.element_identifier) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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21 #set $safe_name = re.sub('[^\w\-\.]', '_', $identifier) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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22 ## Add extension only if filename doesn't already have appropriate extension |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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changeset
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23 #if $input_file.is_of_type('fasta.gz') and not ($safe_name.endswith('.fa.gz') or $safe_name.endswith('.fasta.gz')) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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24 #set $safe_name = $safe_name + '.fa.gz' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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25 #elif $input_file.is_of_type('fasta') and not ($safe_name.endswith('.fa') or $safe_name.endswith('.fasta')) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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26 #set $safe_name = $safe_name + '.fa' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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27 #elif $input_file.is_of_type('fastqsanger.gz', 'fastq.gz') and not ($safe_name.endswith('.fq.gz') or $safe_name.endswith('.fastq.gz')) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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28 #set $safe_name = $safe_name + '.fq.gz' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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29 #elif $input_file.is_of_type('fastqsanger', 'fastq') and not ($safe_name.endswith('.fq') or $safe_name.endswith('.fastq')) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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30 #set $safe_name = $safe_name + '.fq' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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31 #elif $input_file.is_of_type('bam') and not $safe_name.endswith('.bam') |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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32 #set $safe_name = $safe_name + '.bam' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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33 #elif $input_file.is_of_type('cram') and not $safe_name.endswith('.cram') |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
changeset
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34 #set $safe_name = $safe_name + '.cram' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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35 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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changeset
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36 ln -sf '${input_file}' '${safe_name}' && |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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37 #silent $input_files.append($safe_name) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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38 #end for |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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39 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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changeset
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40 ## Run telogator |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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41 telogator2 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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42 -i #echo ' '.join($input_files) |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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43 -o output_dir |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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44 -r '${read_type}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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45 -p "\${GALAXY_SLOTS:-1}" |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
diff
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46 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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47 ## Basic parameters |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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48 -l '${basic_params.min_read_length}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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49 -c '${basic_params.min_canonical_hits}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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50 -n '${basic_params.min_reads_cluster}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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51 -m '${basic_params.atl_method}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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52 #if str($basic_params.downsample) != '' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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53 -d '${basic_params.downsample}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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54 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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55 #if str($basic_params.random_seed) != '' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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56 --rng '${basic_params.random_seed}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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57 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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58 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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59 ## Reference files |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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60 #if $reference_opts.custom_reference |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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61 -t '${reference_opts.custom_reference}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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62 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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63 #if $reference_opts.kmer_file |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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64 -k '${reference_opts.kmer_file}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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65 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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66 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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67 ## Aligner selection |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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68 #if $aligner.aligner_choice == 'minimap2' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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69 --minimap2 minimap2 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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70 #elif $aligner.aligner_choice == 'winnowmap' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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71 --winnowmap winnowmap |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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72 #if $aligner.winnowmap_k15 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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73 --winnowmap-k15 '${aligner.winnowmap_k15}' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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74 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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75 #elif $aligner.aligner_choice == 'pbmm2' |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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76 --pbmm2 pbmm2 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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77 #end if |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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78 |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
parents:
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79 ## Advanced filtering |
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afcb889cbce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
iuc
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80 --filt-tel '${advanced.filtering.filt_tel}' |
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81 --filt-nontel '${advanced.filtering.filt_nontel}' |
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82 --filt-sub '${advanced.filtering.filt_sub}' |
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83 --collapse-hom '${advanced.filtering.collapse_hom}' |
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84 |
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85 ${advanced.filtering.fast_aln} |
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86 |
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87 ## Hierarchical clustering parameters |
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88 -t0 '${advanced.clustering.t0}' |
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89 -t1 '${advanced.clustering.t1}' |
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90 -t2 '${advanced.clustering.t2}' |
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91 -tc '${advanced.clustering.tc}' |
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92 -ts '${advanced.clustering.ts}' |
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93 -th '${advanced.clustering.th}' |
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94 |
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95 ## Plot customization |
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96 -afa-x '${advanced.plotting.afa_x}' |
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97 -afa-t '${advanced.plotting.afa_t}' |
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98 -afa-a '${advanced.plotting.afa_a}' |
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99 -va-y '${advanced.plotting.va_y}' |
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100 -va-t '${advanced.plotting.va_t}' |
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101 -va-p '${advanced.plotting.va_p}' |
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102 |
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103 ## Move outputs to expected locations |
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104 && mv output_dir/tlens_by_allele.tsv '${output_tsv}' |
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105 && mv output_dir/all_final_alleles.png '${output_alleles_plot}' |
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106 && mv output_dir/violin_atl.png '${output_violin_plot}' |
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107 ]]></command> |
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108 <inputs> |
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109 <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."/> |
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110 |
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111 <param name="read_type" type="select" label="Read type" help="Sequencing platform type"> |
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112 <option value="ont">Oxford Nanopore (ONT)</option> |
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113 <option value="hifi" selected="true">PacBio HiFi</option> |
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114 </param> |
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115 |
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116 <section name="basic_params" title="Basic Parameters" expanded="true"> |
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117 <param name="min_read_length" argument="-l" type="integer" value="4000" min="0" label="Minimum read length" help="Minimum read length in base pairs"/> |
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118 <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"/> |
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119 <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"/> |
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120 <param name="atl_method" argument="-m" type="select" label="ATL calculation method" help="Method for calculating allele-specific telomere length"> |
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121 <option value="p75" selected="true">75th percentile (p75)</option> |
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122 <option value="mean">Mean</option> |
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123 <option value="median">Median</option> |
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124 <option value="max">Maximum</option> |
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125 </param> |
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126 <param name="downsample" argument="-d" type="integer" optional="true" value="" label="Downsample telomere reads" help="Downsample to N telomere reads (optional)"/> |
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127 <param name="random_seed" argument="--rng" type="integer" optional="true" value="" label="Random seed" help="Random seed value for reproducibility (optional)"/> |
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128 </section> |
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129 |
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130 <section name="reference_opts" title="Reference Options" expanded="false"> |
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131 <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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132 <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."/> |
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133 </section> |
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134 |
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135 <conditional name="aligner"> |
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136 <param name="aligner_choice" type="select" label="Alignment tool" help="Select which aligner to use"> |
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137 <option value="minimap2" selected="true">minimap2</option> |
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138 <option value="winnowmap">winnowmap</option> |
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139 <option value="pbmm2">pbmm2</option> |
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140 </param> |
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141 <when value="minimap2"/> |
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142 <when value="winnowmap"> |
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143 <param argument="--winnowmap-k15" type="data" format="txt" optional="true" label="Winnowmap k15 file" help="High-frequency kmers file for winnowmap"/> |
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144 </when> |
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145 <when value="pbmm2"/> |
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146 </conditional> |
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147 |
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148 <section name="advanced" title="Advanced Parameters" expanded="false"> |
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149 <section name="filtering" title="Filtering Thresholds" expanded="true"> |
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150 <param argument="--filt-tel" type="integer" value="400" min="0" label="Minimum terminating telomere" help="Minimum terminating telomere length in bp"/> |
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151 <param argument="--filt-nontel" type="integer" value="100" min="0" label="Maximum terminating non-telomere" help="Maximum terminating non-telomere length in bp"/> |
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152 <param argument="--filt-sub" type="integer" value="1000" min="0" label="Minimum terminating subtelomere" help="Minimum terminating subtelomere length in bp"/> |
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153 <param argument="--collapse-hom" type="integer" value="1000" min="0" label="Collapse homologous alleles" help="Merge alleles within this distance in bp"/> |
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154 <param argument="--fast-aln" type="boolean" truevalue="--fast-aln" falsevalue="" checked="false" label="Use fast alignment" help="Use faster but less accurate pairwise alignment"/> |
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155 </section> |
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156 |
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157 <section name="clustering" title="Hierarchical Clustering (TREECUT) Parameters" expanded="false"> |
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158 <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"/> |
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159 <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"/> |
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160 <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"/> |
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161 <param argument="-tc" type="float" value="0.050" min="0" max="1" label="TVR clustering collapse" help="Threshold for collapsing TVR clusters"/> |
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162 <param argument="-ts" type="float" value="0.200" min="0" max="1" label="Subtel cluster refinement" help="Threshold for subtelomere cluster refinement"/> |
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163 <param argument="-th" type="float" value="0.050" min="0" max="1" label="Collapsing aligned alleles" help="Threshold for collapsing aligned alleles"/> |
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164 </section> |
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165 |
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166 <section name="plotting" title="Plot Customization" expanded="false"> |
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167 <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"/> |
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168 <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"/> |
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169 <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"/> |
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170 <param argument="-va-y" type="integer" value="20000" min="0" label="Violin plot Y-axis max" help="Maximum Y-axis value for violin plot"/> |
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171 <param argument="-va-t" type="integer" value="5000" min="0" label="Violin plot tick steps" help="Tick step size for violin plot"/> |
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172 <param argument="-va-p" type="integer" value="2" min="1" label="Ploidy" help="Number of alleles per chromosome arm (ploidy)"/> |
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173 </section> |
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174 </section> |
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175 </inputs> |
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176 <outputs> |
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177 <data name="output_tsv" format="tabular" label="${tool.name} on ${on_string}: Telomere lengths by allele"/> |
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178 <data name="output_alleles_plot" format="png" label="${tool.name} on ${on_string}: All final alleles plot"/> |
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179 <data name="output_violin_plot" format="png" label="${tool.name} on ${on_string}: Violin plot"/> |
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180 </outputs> |
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181 <tests> |
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182 <!-- Test 1: PacBio HiFi data --> |
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183 <test expect_num_outputs="3"> |
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184 <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> |
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185 <param name="read_type" value="hifi"/> |
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186 <conditional name="aligner"> |
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187 <param name="aligner_choice" value="minimap2"/> |
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188 </conditional> |
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189 <output name="output_tsv"> |
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190 <assert_contents> |
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191 <has_text text="chr"/> |
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192 <has_text text="position"/> |
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193 <has_text text="allele_id"/> |
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194 <has_text text="TL_p75"/> |
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195 <has_n_columns n="11"/> |
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196 <has_n_lines n="13" delta="2"/> |
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197 <has_line_matching expression="chr\d+[pq]\t\d+.*"/> |
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198 </assert_contents> |
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199 </output> |
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200 <output name="output_alleles_plot"> |
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201 <assert_contents> |
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202 <has_size min="10000" max="500000"/> |
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203 </assert_contents> |
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204 </output> |
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205 <output name="output_violin_plot"> |
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206 <assert_contents> |
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207 <has_size min="10000" max="500000"/> |
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208 </assert_contents> |
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209 </output> |
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210 </test> |
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211 <!-- Test 2: Oxford Nanopore data, 2 inputs --> |
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212 <test expect_num_outputs="3"> |
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213 <param name="input_reads" value="hg002-ont-1p.fa.gz,hg002-ont-1p.sub.fa.gz"/> |
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214 <param name="read_type" value="ont"/> |
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215 <conditional name="aligner"> |
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216 <param name="aligner_choice" value="minimap2"/> |
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217 </conditional> |
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218 <output name="output_tsv"> |
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219 <assert_contents> |
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220 <has_text text="chr"/> |
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221 <has_text text="position"/> |
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222 <has_text text="allele_id"/> |
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223 <has_text text="TL_p75"/> |
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224 <has_n_columns n="11"/> |
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225 <has_n_lines n="2" delta="10"/> |
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226 </assert_contents> |
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227 </output> |
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228 <output name="output_alleles_plot"> |
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229 <assert_contents> |
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230 <has_size min="10000" max="500000"/> |
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231 </assert_contents> |
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232 </output> |
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233 <output name="output_violin_plot"> |
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234 <assert_contents> |
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235 <has_size min="10000" max="500000"/> |
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236 </assert_contents> |
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237 </output> |
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238 </test> |
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239 <!-- Test 3: PacBio HiFi data, pbmm2 --> |
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240 <test expect_num_outputs="3"> |
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241 <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> |
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242 <param name="read_type" value="hifi"/> |
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243 <conditional name="aligner"> |
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244 <param name="aligner_choice" value="pbmm2"/> |
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245 </conditional> |
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246 <output name="output_tsv"> |
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247 <assert_contents> |
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248 <has_text text="chr"/> |
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249 <has_text text="position"/> |
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250 <has_text text="allele_id"/> |
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251 <has_text text="TL_p75"/> |
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252 <has_n_columns n="11"/> |
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253 <has_n_lines n="13" delta="2"/> |
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254 </assert_contents> |
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255 </output> |
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256 <output name="output_alleles_plot"> |
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257 <assert_contents> |
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258 <has_size min="10000" max="500000"/> |
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259 </assert_contents> |
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260 </output> |
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261 <output name="output_violin_plot"> |
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262 <assert_contents> |
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263 <has_size min="10000" max="500000"/> |
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264 </assert_contents> |
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265 </output> |
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266 </test> |
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267 <!-- Test 4: PacBio HiFi data, winnowmap --> |
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268 <test expect_num_outputs="3"> |
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269 <param name="input_reads" value="hg002-telreads_pacbio.sub.fa.gz"/> |
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270 <param name="read_type" value="hifi"/> |
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271 <conditional name="aligner"> |
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272 <param name="aligner_choice" value="winnowmap"/> |
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273 </conditional> |
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274 <output name="output_tsv"> |
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275 <assert_contents> |
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276 <has_text text="chr"/> |
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277 <has_text text="position"/> |
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278 <has_text text="allele_id"/> |
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279 <has_text text="TL_p75"/> |
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280 <has_n_columns n="11"/> |
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281 <has_n_lines n="13" delta="2"/> |
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282 </assert_contents> |
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283 </output> |
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284 <output name="output_alleles_plot"> |
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285 <assert_contents> |
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286 <has_size min="10000" max="500000"/> |
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287 </assert_contents> |
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288 </output> |
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289 <output name="output_violin_plot"> |
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290 <assert_contents> |
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291 <has_size min="10000" max="500000"/> |
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292 </assert_contents> |
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293 </output> |
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294 </test> |
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295 </tests> |
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296 <help><![CDATA[ |
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297 **What it does** |
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298 |
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299 Telogator2 measures allele-specific telomere length (ATL) and characterizes telomere variant repeat (TVR) sequences from long-read sequencing data (PacBio HiFi or Oxford Nanopore). |
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300 |
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301 The tool performs the following analyses: |
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302 |
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303 1. Extracts reads containing telomeric sequences |
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304 2. Aligns reads to reference genome to identify chromosome arms |
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305 3. Clusters reads by TVR sequences to identify individual alleles |
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306 4. Calculates allele-specific telomere lengths |
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307 5. Generates visualizations of telomere length distributions |
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308 |
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309 **Inputs** |
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310 |
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311 - Long-read sequencing data (FASTA, FASTQ, BAM, or CRAM format) |
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312 - Optional custom reference genome and kmer files |
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313 - Platform-specific parameters (PacBio HiFi or Oxford Nanopore) |
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314 |
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315 **Outputs** |
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316 |
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317 1. **tlens_by_allele.tsv**: Primary results table containing: |
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318 |
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319 - chr: Chromosome arm (or chrU for unmapped) |
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320 - position: Anchor coordinate |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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321 - ref_samp: Reference contig alignment |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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322 - allele_id: Allele identifier (suffix 'i' indicates interstitial telomeric regions) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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323 - TL_p75: Allele-specific telomere length (75th percentile by default) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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324 - read_TLs, read_lengths, read_mapq: Per-read metrics |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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325 - tvr_len, tvr_consensus: Telomere variant repeat characteristics |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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326 - supporting_reads: Read identifiers |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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327 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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328 2. **all_final_alleles.png**: Visualization of all identified alleles |
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329 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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330 3. **violin_atl.png**: Violin plot showing ATL distributions by chromosome arm |
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331 |
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332 **Platform-Specific Recommendations** |
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333 |
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334 - **PacBio Revio HiFi (30x coverage)**: Set minimum reads per cluster to 4 |
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335 - **PacBio Sequel II (10x coverage)**: Set minimum reads per cluster to 3 |
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336 - **Nanopore R10 (30x coverage)**: Set minimum reads per cluster to 4 |
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337 - **Large enrichment datasets**: Increase minimum reads per cluster to 10 |
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338 |
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339 **Important Notes** |
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340 |
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341 - For PacBio Revio data, include both "hifi" and "fail" BAM files |
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342 - Older Nanopore data (Guppy basecalled) may have high error rates in telomere regions |
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343 - Runtime improves with additional CPU cores (increase processes parameter) |
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344 - Alleles with suffix 'i' are interstitial telomeric regions and may need to be excluded from downstream analysis |
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345 |
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346 ]]></help> |
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347 <expand macro="citations"/> |
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348 </tool> |