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annotate teloscope.xml @ 0:be2c72b9798b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
author iuc
date Thu, 27 Nov 2025 08:52:19 +0000
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children 089c6e8122c8
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0
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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1 <tool id="teloscope" name="Teloscope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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2 <description>Assembly telomere annotation</description>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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3 <macros>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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4 <import>macros.xml</import>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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5 </macros>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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6 <expand macro="requirements"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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7 <version_command>teloscope -v</version_command>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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8 <command detect_errors="exit_code"><![CDATA[
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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9 mkdir -p output &&
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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10 teloscope
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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11 --input-sequence '$input_sequence'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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12 --output output
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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13 --canonical '$canonical'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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14 --patterns '$patterns'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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15 --window '$window'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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16 --step '$step'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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17 --threads "\${GALAXY_SLOTS:-2}"
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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18 --terminal-limit '$terminal_limit'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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19 --max-match-distance '$max_match_distance'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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20 --max-block-distance '$max_block_distance'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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21 --min-block-length '$min_block_length'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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22 --min-block-density '$min_block_density'
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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23
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24 $out_win_repeats
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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25 $out_gc
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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26 $out_entropy
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27 $out_matches
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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28 $out_its
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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29 $ultra_fast
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30 $verbose
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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31 > output/${input_sequence.name}.telo.report
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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32 ]]></command>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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33 <inputs>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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34 <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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35 <param argument="--canonical" type="text" value="TTAGGG" label="Canonical telomeric pattern">
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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36 <sanitizer>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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37 <valid initial="string.printable">
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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38 <remove value=" "/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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39 <remove value="\t"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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40 <remove value="\r"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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41 <remove value="\n"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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42 </valid>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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43 </sanitizer>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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44 <validator type="regex" message="Canonical must contain only A,C,G,T.">^[ACGTacgt]+$</validator>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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45 </param>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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46
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47 <param argument="--patterns" type="text" value="TTAGGG,CCCTAA"
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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48 label="Patterns to explore (comma-separated), IUPAC allowed">
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49 <validator type="regex"
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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50 message="Use IUPAC letters ACGTRYSWKMBDHVN; comma-separated.">^[ACGTRYSWKMBDHVNacgtryswkmbdhvn]+(?:,[ACGTRYSWKMBDHVNacgtryswkmbdhvn]+)*$</validator>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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51 </param>
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52
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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53 <param argument="--window" type="integer" min="100" value="1000" label="Sliding window size"/>
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54 <param argument="--step" type="integer" min="100" value="500" label="Sliding window step"/>
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55 <param argument="--terminal-limit" type="integer" min="10000" value="50000" label="Terminal limit (bp) in contigs"/>
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56 <param argument="--max-match-distance" type="integer" min="0" value="50" label="Maximum distance (bp) for merging matches"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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57 <param argument="--max-block-distance" type="integer" min="0" value="200" label="Maximum block distance for merging"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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58 <param argument="--min-block-length" type="integer" min="0" value="500" label="Minimum block length"/>
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59 <param argument="--min-block-density" type="float" min="0" max="1" value="0.5" label="Minimum block density (0–1)"/>
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60
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61 <param argument="--out-win-repeats" type="boolean" truevalue="--out-win-repeats" falsevalue="" checked="false" label="Window repeat counts"/>
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62 <param argument="--out-gc" type="boolean" truevalue="--out-gc" falsevalue="" checked="false" label="Window GC"/>
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63 <param argument="--out-entropy" type="boolean" truevalue="--out-entropy" falsevalue="" checked="false" label="Window Shannon entropy"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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64 <param argument="--out-matches" type="boolean" truevalue="--out-matches" falsevalue="" checked="false" label="Canonical/NonCanonical Matches"/>
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65 <param argument="--out-its" type="boolean" truevalue="--out-its" falsevalue="" checked="false" label="Interstitial telomeres (ITSs)"/>
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66 <param argument="--ultra-fast" type="boolean" truevalue="--ultra-fast" falsevalue="" checked="true" label="Ultra-fast mode (terminal regions only)"/>
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67 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose output"/>
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68 </inputs>
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69
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70 <outputs>
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71 <!-- BASIC OUTFILES -->
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72 <data name="terminal_telomeres" format="bed" from_work_dir="output/*_terminal_telomeres.bed" label="${tool.name} on ${on_string}: Terminal telomeres"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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73 <data name="telo_report" format="tabular" from_work_dir="output/*.telo.report" label="${tool.name} on ${on_string}: Summary report"/>
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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74
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75 <!-- OPTIONAL OUTFILES -->
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76 <data name="interstitial_telomeres" format="bed" from_work_dir="output/*_interstitial_telomeres.bed" label="${tool.name} on ${on_string}: Interstitial telomeres">
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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77 <filter>out_its</filter>
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78 </data>
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79 <data name="canonical_matches" format="bed" from_work_dir="output/*_canonical_matches.bed" label="${tool.name} on ${on_string}: Canonical matches">
be2c72b9798b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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80 <filter>out_matches</filter>
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81 </data>
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82 <data name="noncanonical_matches" format="bed" from_work_dir="output/*_noncanonical_matches.bed" label="${tool.name} on ${on_string}: Noncanonical matches">
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83 <filter>out_matches</filter>
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84 </data>
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85 <data name="window_metrics" format="bedgraph" from_work_dir="output/*_window_metrics.bedgraph" label="${tool.name} on ${on_string}: Window metrics">
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86 <filter>out_gc or out_entropy or out_win_repeats</filter>
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87 </data>
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88 </outputs>
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89
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90 <tests>
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91 <!-- 1) Default (-u) : terminal telomeres + report -->
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92 <test expect_num_outputs="2">
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93 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
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94 <param name="canonical" value="TTAGGG"/>
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95 <param name="patterns" value="TTAGGG,CCCTAA"/>
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96 <output name="terminal_telomeres">
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97 <assert_contents>
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98 <!-- at least one BED-like line (match whole line to allow extra cols) -->
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99 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/>
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100 </assert_contents>
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101 </output>
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102 <output name="telo_report">
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103 <assert_contents>
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104 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
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105 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/>
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106 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/>
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107 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/>
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108 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112
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113 <!-- 2) Genome-wide (-g -e -r -m -i ; disable -u) -->
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114 <test expect_num_outputs="6">
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115 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
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116 <param name="canonical" value="TTAGGG"/>
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117 <param name="patterns" value="TTAGGG,CCCTAA"/>
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118 <param name="out_gc" value="true"/>
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119 <param name="out_entropy" value="true"/>
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120 <param name="out_win_repeats" value="true"/>
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121 <param name="out_matches" value="true"/>
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122 <param name="out_its" value="true"/>
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123 <param name="ultra_fast" value="false"/>
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124
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125 <output name="terminal_telomeres">
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126 <assert_contents>
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127 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/>
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128 </assert_contents>
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129 </output>
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130 <output name="interstitial_telomeres">
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131 <assert_contents>
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132 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/>
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133 </assert_contents>
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134 </output>
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135 <output name="canonical_matches">
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136 <assert_contents>
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137 <!-- ensure at least one CCCTAA match line -->
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138 <has_line_matching expression="^\S+\t\d+\t\d+\tCCCTAA(?:\s|$)"/>
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139 </assert_contents>
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140 </output>
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141 <output name="noncanonical_matches">
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142 <assert_contents>
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143 <!-- expect an empty file -->
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144 <has_n_lines n="0"/>
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145 </assert_contents>
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146 </output>
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147 <output name="window_metrics">
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148 <assert_contents>
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149 <has_text text="track type=bedGraph"/>
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150 <!-- first data window line -->
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151 <has_line_matching expression="^\S+\t0\t1000\t.*"/>
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152 </assert_contents>
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153 </output>
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154 <output name="telo_report">
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155 <assert_contents>
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156 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
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157 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/>
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158 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/>
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159 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/>
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160 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/>
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161 </assert_contents>
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162 </output>
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163 </test>
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164 </tests>
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165
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166 <help><![CDATA[
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167 Description:
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168 Teloscope is a tool for telomere annotation in genome assemblies.
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169 It scans for user-specified telomeric repeat patterns across assembly paths, contigs and windows.
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170 Teloscope annotates terminal and interstitial telomeres, canonical/noncanonical matches and genome-wide metrics such as GC content, Shannon entropy, and repeat counts.
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171 It generates a detailed telomere summary report for paths, telomere statistics, and chromosome labels to assess telomere completeness.
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172 Teloscope can be used for both complete and fragmented assemblies, providing valuable information for genome manual curation and analysis.
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173
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174 Usage:
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175 Default (ultra-fast) scans terminal regions and reports terminal telomeres + a summary report.
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176 * ${input_sequence.name}_terminal_telomeres.bed
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177 * ${input_sequence.name}.telo.report
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178
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179 Enabling window/match options (-g -e -r -m -i) performs a genome-wide scan and produces:
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180 * ${input_sequence.name}_terminal_telomeres.bed
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181 * ${input_sequence.name}_interstitial_telomeres.bed
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182 * ${input_sequence.name}_canonical_matches.bed
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183 * ${input_sequence.name}_noncanonical_matches.bed
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184 * ${input_sequence.name}_window_metrics.bedgraph
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185 * ${input_sequence.name}.telo.report
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186
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187 Key parameters:
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188 - -c / --canonical: Canonical repeat (default TTAGGG). This is the vertebrate telomeric motif found at chromosome ends that binds to shelterin complex to form a telomere.
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189 - -p / --patterns: Variant patterns (comma-separated). These are additional telomeric repeat motifs to search for, besides the canonical repeat, it includes other variants that can be part of telomeres.
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190 - -w / -s: window size / step (defaults 1000/500)
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191 - -u / --ultra-fast: terminal scan only (default true); disabled automatically when -g/-e/-r/-m/-i are used.
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192 ]]></help>
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193
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194 <expand macro="citations"/>
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195 </tool>