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annotate microsatbed.xml @ 1:dddd7ef63469 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 4f8728c5e0a135c14a0df7d6788e8069b19cc215
author iuc
date Thu, 25 Jul 2024 06:03:17 +0000
parents 2b970db61912
children 3f6e5c701945
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2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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2 <tool id="microsatbed" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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3 <description>Short Tandem Repeats to bed features from fasta</description>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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4 <macros>
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5 <token name="@TOOL_VERSION@">1.3.2</token>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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6 <token name="@VERSION_SUFFIX@">0</token>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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7 <token name="@PYTHON_VERSION@">3.12.3</token>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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8 <macro name="subsetmacro">
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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9 <param name="subset" type="select" label="Select at least 1 specific motif length to report" help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more" multiple="true">
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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10 <option value="--di" selected="true">All dimers (AC,AG,AT,...)</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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11 <option value="--tri">All trimers (ACG,..)</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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12 <option value="--tetra">All tetramers (ACGT,..)</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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13 <option value="--penta">All pentamers (ACGTC,..)</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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14 <option value="--hexa">All hexamers (ACGTCG,..)</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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15 <option value="--mono">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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16 </param>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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17 </macro>
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18 </macros>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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19 <requirements>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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20 <requirement version="@PYTHON_VERSION@" type="package">python</requirement>
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dddd7ef63469 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 4f8728c5e0a135c14a0df7d6788e8069b19cc215
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21 <requirement version="2.1.0" type="package">pyfastx</requirement>
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22 <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement>
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dddd7ef63469 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 4f8728c5e0a135c14a0df7d6788e8069b19cc215
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23 <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
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24 </requirements>
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25 <required_files>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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26 <include path="find_str.py"/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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27 </required_files>
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28 <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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29 <command><![CDATA[
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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30 #if $mode_cond.mode == "NATIVE":
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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31 #if $reference_genome.genome_type_select == "history":
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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32 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta}'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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33 #else:
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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34 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta.fields.path}'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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35 #end if
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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36 #else:
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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37 python '${__tool_directory__}/find_str.py'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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38 #if $reference_genome.genome_type_select == "history":
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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39 --fasta '${reference_genome.fasta}'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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40 #else:
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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41 --fasta '${reference_genome.fasta.fields.path}'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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42 #end if
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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43 --bed '$bed'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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44 #if $mode_cond.mode == "SPECIFIC":
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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45 --specific '$mode_cond.specific'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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46 #elif $mode_cond.mode == "SPECIFICBW":
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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47 --bigwig
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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48 --winwidth '$mode_cond.winwidth'
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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49 --specific '$mode_cond.specific'
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50 #else:
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51 #for $flag in $mode_cond.subset:
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52 $flag
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53 #end for
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54 #end if
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55 --monomin '$monomin'
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56 --dimin '$dimin'
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57 --trimin '$trimin'
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58 --tetramin '$tetramin'
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59 --pentamin '$pentamin'
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60 --hexamin '$hexamin'
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61 #if $mode_cond.mode == "SPECIFICBW":
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62 --bigwig
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63 --winwidth '$mode_cond.winwidth'
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64 #end if
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65 #end if
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66 ]]></command>
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67 <inputs>
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68 <conditional name="reference_genome">
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69 <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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70 <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
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71 <option value="history" selected="True">Use any fasta file from the current history</option>
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72 </param>
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73 <when value="indexed">
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74 <param name="fasta" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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75 <options from_data_table="all_fasta"/>
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76 </param>
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77 </when>
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78 <when value="history">
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79 <param name="fasta" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
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80 </when>
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81 </conditional>
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82 <conditional name="mode_cond">
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83 <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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84 <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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85 <option value="ALLBW">By length as windowed bigwig: Report all motifs of one or more specified lengths (1-6nt) as windowed density</option>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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86 <option value="SPECIFIC">By motif: Report one or more specific motifs (such as TCA,GC) as bed features</option>
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87 <option value="SPECIFICBW">By motif as windowed bigwig: Report one or more specific motifs (such as TCA,GC) as windowed density</option>
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88 <option value="NATIVE">All exact STR: use the pytrf findstr native command to a create csv, tsv or gtf output</option>
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89 </param>
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90 <when value="ALL">
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91 <expand macro="subsetmacro"/>
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92 </when>
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93 <when value="ALLBW">
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94 <expand macro="subsetmacro"/>
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95 <param name="winwidth" type="integer" min="5" value="128" label="Window with for estimating STR bigwig density"/>
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96 </when>
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97 <when value="SPECIFIC">
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98 <param name="specific" type="text" label="Supply a specific motif pattern. Separate multiple patterns with commas such as GA,GC" help="Make bed features only for the nominated specific motifs."/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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99 </when>
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100 <when value="SPECIFICBW">
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101 <param name="specific" type="text" label="Supply a specific motif pattern. Separate multiple patterns with commas such as GA,GC" help="Make bed features only for the nominated specific motifs."/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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102 <param name="winwidth" type="integer" min="5" value="128" label="Window with for estimating STR bigwig density"/>
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103 </when>
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104 <when value="NATIVE">
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105 <param name="outformat" type="select" label="Select the required output format" help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below">
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106 <option value="gff">GFF</option>
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107 <option value="csv">Comma separated values</option>
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108 <option value="tsv" selected="true">Tab separated values</option>
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109 </param>
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110 </when>
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111 </conditional>
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112 <param name="monomin" type="integer" min="2" value="10" label="Minimum repeats required for monomers"/>
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113 <param name="dimin" type="integer" min="1" value="3" label="Minimum repeats required for dimers"/>
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114 <param name="trimin" type="integer" min="2" value="2" label="Minimum repeats required for trimers"/>
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115 <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
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116 <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
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117 <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
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118 </inputs>
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119 <outputs>
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120 <data name="bed" format="bed" label="STR from $fasta.element_identifier">
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121 <change_format>
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122 <when input="mode_cond.outformat" value="gff" format="gff"/>
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123 <when input="mode_cond.outformat" value="csv" format="csv"/>
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124 <when input="mode_cond.outformat" value="tsv" format="tabular"/>
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125 <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>
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126 <when input="mode_cond.mode" value="SPECIFICBW" format="bigwig"/>
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127 </change_format>
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128 </data>
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129 </outputs>
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130 <tests>
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131 <test expect_num_outputs="1">
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132 <conditional name="reference_genome">
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133 <param name="genome_type_select" value="history"/>
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134 <param name="fasta" value="humsamp.fa"/>
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135 </conditional>
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136 <conditional name="mode_cond">
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137 <param name="mode" value="ALL"/>
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138 <param name="subset" value="--di,--tri,--tetra,--penta,--hexa"/>
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139 </conditional>
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140 <param name="monomin" value="20"/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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141 <param name="dimin" value="20"/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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142 <param name="trimin" value="5"/>
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143 <param name="tetramin" value="5"/>
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144 <param name="pentamin" value="3"/>
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145 <param name="hexamin" value="2"/>
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146 <output name="bed" value="bed_sample" compare="diff" lines_diff="0">
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147 <assert_contents>
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148 <has_n_columns n="5"/>
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149 <has_text text="hpat1"/>
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150 <has_text text="CCCCAC_2"/>
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151 <has_text text="TTTTTT_2"/>
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152 </assert_contents>
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153 </output>
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154 </test>
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155 <test expect_num_outputs="1">
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156 <conditional name="reference_genome">
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157 <param name="genome_type_select" value="history"/>
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158 <param name="fasta" value="humsamp.fa"/>
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159 </conditional>
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160 <conditional name="mode_cond">
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161 <param name="mode" value="SPECIFIC"/>
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162 <param name="specific" value="GC"/>
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163 </conditional>
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164 <param name="monomin" value="20"/>
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165 <param name="dimin" value="1"/>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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166 <param name="trimin" value="20"/>
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167 <param name="tetramin" value="20"/>
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168 <param name="pentamin" value="20"/>
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169 <param name="hexamin" value="20"/>
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170 <output name="bed" value="dibed_sample" compare="diff" lines_diff="0">
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171 <assert_contents>
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172 <has_n_columns n="5"/>
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173 <has_text text="hpat1"/>
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174 <has_text text="GC_1"/>
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175 <not_has_text text="TC_1"/>
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176 <has_text text="209316"/>
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177 </assert_contents>
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178 </output>
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179 </test>
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180 <test expect_num_outputs="1">
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181 <conditional name="reference_genome">
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182 <param name="genome_type_select" value="history"/>
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183 <param name="fasta" value="mouse.fa"/>
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184 </conditional>
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185 <conditional name="mode_cond">
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186 <param name="mode" value="NATIVE"/>
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187 <param name="outformat" value="gff"/>
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188 </conditional>
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189 <param name="monomin" value="20"/>
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190 <param name="dimin" value="10"/>
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191 <param name="trimin" value="5"/>
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192 <param name="tetramin" value="4"/>
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193 <param name="pentamin" value="4"/>
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194 <param name="hexamin" value="2"/>
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195 <output name="bed" value="nativegff_sample" compare="diff" lines_diff="0">
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196 <assert_contents>
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197 <has_n_columns n="9"/>
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198 <has_text text="Motif=CCGCCG;Type=6;Repeat=2;Length=12"/>
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199 <has_text text="mm10_knownGene_uc008xda.1"/>
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200 <has_text text="Motif=AGAGAG;Type=6;Repeat=2;Length=12"/>
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201 </assert_contents>
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202 </output>
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203 </test>
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204 <test expect_num_outputs="1">
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205 <conditional name="reference_genome">
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206 <param name="genome_type_select" value="history"/>
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207 <param name="fasta" value="humsamp.fa"/>
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208 </conditional>
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209 <conditional name="mode_cond">
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210 <param name="mode" value="SPECIFICBW"/>
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211 <param name="specific" value="GC"/>
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212 </conditional>
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213 <param name="monomin" value="20"/>
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214 <param name="dimin" value="1"/>
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215 <param name="trimin" value="20"/>
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216 <param name="tetramin" value="20"/>
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217 <param name="pentamin" value="20"/>
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218 <param name="hexamin" value="20"/>
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219 <output name="bed" value="dibed_wig_sample" compare="sim_size" delta="10">
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220 <assert_contents>
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221 <has_size value="73544" delta="10" />
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222 </assert_contents>
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223 </output>
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224 </test>
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225 </tests>
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226 <help><![CDATA[
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227
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228 **Convert short repetitive sequences to bed features or windowed density bigwigs**
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229
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230 Microsatellites are usually defined as repeated short DNA patterns in an unbroken sequence.
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231 A microsatellite pattern or *motif* can be any combination nucleotides, typically from 1 to 6nt in length.
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232
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233 This tool allows microsatellite and related features to be selected from a fasta sequence input file, and output into a track, suitable for viewing in a genome browser such as JBrowse2.
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234
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235 All motifs of selected lengths can be reported as individual features in the output bed file, or specific motifs can be provided and all
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236 others will be ignored. In all cases, a minimum required number of repeats can be specified. For example, requiring 2 or more repeats of the trimer *ACG* will report
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237 every sequence of *ACGACG* or *ACGACGACG* or *ACGACGACGACG* and so on, as individual bed features. Similarly, requiring 3 repeats of any trimer will
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238 report every distinct 3 nucleotide pattern, including *ACGACGACG* as well as every other unique 3 nucleotide pattern with 3 sequential repeats or more such, as "CTCCTCCTC*.
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239
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240 For other output formats, the pytrf native command line *findstr* can be used to produce a gff, csv or tsv output containing all exact short tandem repeats, as
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241 described at the end of https://pytrf.readthedocs.io/en/latest
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242
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243 A fasta file must be supplied for processing. A built in genome can be selected, or a fasta file of any kind can be selected from the current history. Note that all
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244 symbols are treated as valid nucleotides by pytrf, so extraneous characters such as *-* or *N* in the input fasta may appear as unexpected bed features. Lower case fasta symbols will be converted
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245 to uppercase, to prevent them being reported as distinct motifs.
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246
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247 Output can be bed format, or for two kinds of operation, a bigwig track showing bases covered by selected features over a configurable window size with a default of 128nt.
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248
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249 **Select motifs by length - for bed or windowed density bigwig**
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250
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251 The default tool form setting is to select all dimer motif patterns.
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252
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253 Any combination of motif lengths from 1 to 6nt can be selected in the multiple-select drop-down list. All features will be returned in a single bed file. For each selected motif length,
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254 the minimum number of repeats required for reporting can be adjusted. **Tandem repeats** are defined as at least 2 of any pattern. This tool allows singleton dimer motifs to be reported,
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255 so is not restricted to short tandem repeats (STR)
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256
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257 This mode of operation can produce a bed file with every STR as a separate feature.
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258 These can be very large and a bigwig containing the sum of STR bases over a selectable window size (default 128) may be more
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259 useful and much faster to load.
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260
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261 **Select motifs by pattern - for bed or windowed density bigwig**
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262
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263 This option allows a motif pattern to be specified as a text string such as *CG* or *ATC*. Multiple motifs can be specified as a comma separated string such as *CG,ATC*.
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264 All features will be returned as a single bed file.
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265
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266 The minimum number of repeats for all motifs can be set to match specific requirements.
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267
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268 For example, technical sequencing read bias may be influenced by the density of specific dimers, whether they are repeated or not
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269 such as in https://github.com/arangrhie/T2T-Polish/tree/master/pattern
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270
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271 This mode of operation can produce a bed file with every STR as a separate feature.
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272 These can be very large and a bigwig containing the sum of STR bases over a selectable window size (default 128) may be more
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273 useful and much faster to load.
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274
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275 **Select all perfect STR using pytrf findstr in csv, tsv or gff output format**
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276
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277 This selection runs the pytrf *findstr* option to create gff/csv/tsv outputs as described at the end of https://pytrf.readthedocs.io/en/latest/.
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278
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279 Quoted here:
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280
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281 *A Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA sequence repeated consecutively. The core sequence or repeat unit is generally called motif.
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282 According to the motif length, tandem repeats can be classified as microsatellites and minisatellites. Microsatellites are also known as simple sequence repeats (SSRs)
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283 or short tandem repeats (STRs) with motif length of 1-6 bp. Minisatellites are also sometimes referred to as variable number of tandem repeats (VNTRs) has longer motif length than microsatellites.
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284 Pytrf is a lightweight Python C extension for identification of tandem repeats. The pytrf enables to fastly identify both exact or perfect SSRs.
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285 It also can find generic tandem repeats with any size of motif, such as with maximum motif length of 100 bp. Additionally, it has capability of finding approximate or imperfect tandem repeats*
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286
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287 ]]></help>
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288 <citations>
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289 <citation type="bibtex">@misc{pytrf,
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290 title = {{pytrf} Short tandem repeat finder, Accessed on July 10 2024},
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291 howpublished = {\url{https://github.com/lmdu/pytrf}},
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292 note = {Accessed on July 10 2024}
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293 }</citation>
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294 </citations>
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295 </tool>