Mercurial > repos > iuc > telogator

annotate telogator_make_ref.xml @ 0:afcb889cbce3 draft default tip

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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
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afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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1 <tool id="telogator_make_ref" name="Telogator Make Reference" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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2 <description>Create custom telogator reference from a T2T assembly</description>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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3 <macros>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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4 <import>macros.xml</import>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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5 </macros>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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6 <expand macro="edam_ontology"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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7 <expand macro="xrefs"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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8 <expand macro="requirements"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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9 <expand macro="version_command"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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10 <command detect_errors="exit_code"><![CDATA[
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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11 #import re
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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12 #set $identifier = str($input_fasta.element_identifier)
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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13 #set $safe_name = re.sub('[^\w\-\.]', '_', $identifier)
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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14 #if $input_fasta.is_of_type('fasta.gz') and not ($safe_name.endswith('.fa.gz') or $safe_name.endswith('.fasta.gz'))
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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15 #set $safe_name = $safe_name + '.fa.gz'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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16 #elif $input_fasta.is_of_type('fasta') and not ($safe_name.endswith('.fa') or $safe_name.endswith('.fasta'))
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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17 #set $safe_name = $safe_name + '.fa'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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18 #end if
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19 mkdir -p output_dir &&
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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20 ln -sf '${input_fasta}' '${safe_name}' &&
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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21 make_telogator_ref
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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22 -i '${safe_name}'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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23 -o output_dir/output_ref.fa
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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24 -s '${sample_name}'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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25 -c '${contig_list}'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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26 ## Optional kmer file
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27 #if $kmer_file
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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28 -k '${kmer_file}'
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29 #end if
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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30 ## Minimum telomere length
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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31 -m '${min_tel_length}'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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32 ## Optional flags
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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33 ${add_tel}
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34 ${plot}
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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35 ## Move outputs
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36 && mv output_dir/output_ref.fa '${output_fasta}'
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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37 ]]></command>
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38 <inputs>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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39 <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)"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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40 <param name="sample_name" argument="-s" type="text" value="sample" label="Sample name" help="Sample name to prepend to contig identifiers in the output">
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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41 <validator type="regex" message="Sample name must contain only alphanumeric characters and hyphens">^[a-zA-Z0-9-]+$</validator>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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42 </param>
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43 <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.">
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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44 <validator type="empty_field"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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45 <sanitizer>
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46 <valid initial="string.printable">
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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47 <remove value="&quot;"/>
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48 </valid>
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49 </sanitizer>
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50 </param>
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51 <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."/>
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52 <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)"/>
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53 <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"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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54 <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"/>
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55 </inputs>
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56 <outputs>
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57 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: Reference FASTA"/>
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58 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Telomere signal plots">
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59 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png$" directory="output_dir" format="png"/>
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60 <filter>plot</filter>
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61 </collection>
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62 </outputs>
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63 <tests>
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64 <!-- Test 1: Basic usage with minimal parameters -->
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65 <test expect_num_outputs="1">
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66 <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz"/>
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67 <param name="sample_name" value="test-sample1"/>
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68 <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"/>
afcb889cbce3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2 commit ff18f7a9e15883099ec1cd699533658a280dcf12
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69 <output name="output_fasta">
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70 <assert_contents>
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71 <has_text text=">test-sample"/>
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72 <has_line_matching expression="^&gt;.*"/>
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73 <has_line_matching expression="^[ACGTN]+$"/>
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74 <has_size value="6100428" delta="100000"/>
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75 <not_has_text text=">test-sample1_tel-"/>
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76 </assert_contents>
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77 </output>
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78 </test>
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79 <!-- Test 2: With plot generation -->
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80 <test expect_num_outputs="2">
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81 <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz"/>
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82 <param name="sample_name" value="test-sample2"/>
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83 <param name="plot" value="true"/>
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84 <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"/>
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85 <output name="output_fasta">
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86 <assert_contents>
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87 <has_text text=">test-sample2"/>
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88 </assert_contents>
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89 </output>
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90 <output_collection name="plots" type="list">
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91 <element name="test-sample2_telsignal_t2t-i002c-mat_chr11pp">
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92 <assert_contents>
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93 <has_size min="10000"/>
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94 </assert_contents>
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95 </element>
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96 <element name="test-sample2_telsignal_t2t-i002c-mat_chr11qq">
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97 <assert_contents>
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98 <has_size min="10000"/>
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99 </assert_contents>
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100 </element>
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101 <element name="test-sample2_telsignal_t2t-i002c-mat_chr12pp">
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102 <assert_contents>
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103 <has_size min="10000"/>
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104 </assert_contents>
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105 </element>
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106 <element name="test-sample2_telsignal_t2t-i002c-mat_chr12qq">
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107 <assert_contents>
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108 <has_size min="10000"/>
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109 </assert_contents>
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110 </element>
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111 <element name="test-sample2_telsignal_t2t-i002c-mat_chr13pp">
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112 <assert_contents>
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113 <has_size min="10000"/>
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114 </assert_contents>
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115 </element>
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116 <element name="test-sample2_telsignal_t2t-i002c-mat_chr13qq">
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117 <assert_contents>
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118 <has_size min="10000"/>
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119 </assert_contents>
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120 </element>
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121 </output_collection>
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122 </test>
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123 <!-- Test 3: use telomere parameters -->
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124 <test expect_num_outputs="1">
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125 <param name="input_fasta" value="t2t_subset_with_telomeres.fa.gz" />
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126 <param name="sample_name" value="test-sample3"/>
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127 <param name="min_tel_length" value="1000"/>
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128 <param name="add_tel" value="true"/>
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129 <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"/>
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130 <output name="output_fasta">
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131 <assert_contents>
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132 <has_text text=">test-sample3"/>
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133 <has_line_matching expression="^&gt;.*"/>
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134 <has_line_matching expression="^[ACGTN]+$"/>
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135 <has_size value="4066952" delta="100000"/>
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136 <has_text text=">test-sample3_tel-"/>
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137 </assert_contents>
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138 </output>
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139 </test>
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140 </tests>
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141 <help><![CDATA[
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142 **What it does**
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143
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144 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.
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145
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146 The tool performs the following steps:
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147
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148 1. Reads the input T2T reference FASTA file
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149 2. Identifies telomeric sequences at contig ends
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150 3. Optionally filters and remaps contigs
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151 4. Creates a processed reference suitable for telogator analysis
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152 5. Generates an index file (.fai) for the reference
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153 6. Optionally generates visualization plots of telomere signals
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154
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155 **When to use this tool**
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156
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157 Use this tool when you need to:
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158
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159 - Analyze telomeres in non-human organisms (e.g., mouse, maize, other species)
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160 - Work with custom or newly assembled T2T genomes
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161 - Create a reference from alternative human T2T assemblies (T2T-yao, T2T-cn1, etc.)
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162 - Prepare references with specific contig selections or naming conventions
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163
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164 **Inputs**
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165
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166 - **T2T reference FASTA**: A telomere-to-telomere reference genome assembly
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167 - **Sample name**: Identifier prepended to contig names (use organism/assembly name)
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168 - **Contig list**: Comma-delimited list of contigs to include (defaults to all human chromosomes)
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169 - **Telomere kmers file** (optional): Custom telomere repeat patterns for non-human organisms
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170 - **Minimum telomere length**: Filter contigs by minimum telomere length at ends
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171
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172 **Outputs**
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173
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174 1. **Reference FASTA**: Processed telogator reference file ready for use with telogator
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175 2. **Reference index (.fai)**: Index file for the created reference FASTA
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176 3. **Telomere signal plots** (optional): PNG plots showing telomere signals for each chromosome arm
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177
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178 **Important Notes**
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179
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180 - The input FASTA should be a high-quality T2T assembly with telomeres at contig ends
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181 - The sample name should be descriptive (e.g., organism name, assembly version), may not contain underscores
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182 - The contig list defaults to human chromosomes; modify it for other organisms or custom assemblies
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183 - For non-human organisms, provide a telomere kmers file matching the species' telomere repeats
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184
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185 ]]></help>
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186 <expand macro="citations"/>
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187 </tool>