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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani commit 2510af3d8a6e812e211ea9fa1ebf42259b7c27f0
author iuc
date Sat, 18 May 2024 15:26:00 +0000
parents 2c7ac12ad75a
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1 <tool id="fastani" name="FastANI" version="@VERSION@">
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2 <description> fast alignment-free computation of whole-genome Average Nucleotide Identity</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
3c6e0e8df873 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani commit 2510af3d8a6e812e211ea9fa1ebf42259b7c27f0
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements" />
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8 <version_command>fastANI --version</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #import re
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12
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13 ### SET UP INPUTS ###
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14 #for $input_q in $query:
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15 #set $file_name = re.sub('[^\w_]', '_', $input_q.element_identifier)
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16 ln -fs '$input_q' '${file_name}_query' &&
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17 echo '${file_name}_query' >> query.lst &&
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18 #end for
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19
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20 #for $input_r in $reference:
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21 #set $file_name = re.sub('[^\w_]', '_', $input_r.element_identifier)
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22 ln -fs '$input_r' '${file_name}_ref' &&
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23 echo '${file_name}_ref' >> ref.lst &&
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24 #end for
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25
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26
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27 ### COMMAND ###
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28
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29 fastANI --ql query.lst --rl ref.lst -o output -t "\${GALAXY_SLOTS:-1}"
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30
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31 ]]></command>
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32 <inputs>
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33 <param name="query" type="data" format="fasta" multiple="true" label="Query Sequence(s)"
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34 help="Specify any number of query sequences in fasta format as input." />
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35 <param name="reference" type="data" format="fasta" multiple="true" label="Reference Sequence(s)"
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36 help="Specify any number of reference sequences in fasta format as input." />
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37 </inputs>
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38 <outputs>
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39 <data name="output" format="tabular" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="query" value="E.coli_1.fasta" />
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44 <param name="reference" value="S.flexneri_1.fasta" />
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45 <output name="output" file="single.out" compare="sim_size" />
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46 </test>
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47 <test>
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48 <param name="query" value="E.coli_1.fasta,E.coli_2.fasta" />
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49 <param name="reference" value="S.flexneri_1.fasta,S.flexneri_2.fasta" />
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50 <output name="output" file="multi.out" compare="sim_size" />
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 FastANI
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56 =======
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57
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58 FastANI is developed for fast alignment-free computation of whole-genome
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59 Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide
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60 identity of orthologous gene pairs shared between two microbial genomes.
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61 FastANI supports pairwise comparison of both complete and draft genome
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62 assemblies. Its underlying procedure follows a similar workflow as described
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63 by `Goris et al. 2007 <https://doi.org/10.1099/ijs.0.64483-0>`_. However, it avoids expensive sequence alignments and
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64 uses `Mashmap <https://github.com/marbl/MashMap>`_ as its MinHash based sequence mapping engine to compute the
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65 orthologous mappings and alignment identity estimates. Based on our
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66 experiments with complete and draft genomes, its accuracy is on par with
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67 `BLAST-based ANI solver <http://enve-omics.ce.gatech.edu/ani/>`_ and it achieves two to three orders of magnitude
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68 speedup. Therefore, it is useful for pairwise ANI computation of large
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69 number of genome pairs. More details about its speed, accuracy and potential
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70 applications are described here: `"High Throughput ANI Analysis of 90K
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71 Prokaryotic Genomes Reveals Clear Species Boundaries" <https://doi-org.uml.idm.oclc.org/10.1038/s41467-018-07641-9>`_.
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72
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73 Please visit the authors at: https://github.com/ParBLiSS/FastANI
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74
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75
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76 Inputs
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77 ------
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78
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79 **Query Sequence(s):**
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80 Input one or more query genomes in fasta format
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81
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82 **Reference Sequence(s):**
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83 Input one or more reference genomes to be compared to the query genomes
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84
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85
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86 Output
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87 ------
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88
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89 Tabular table output with columns: Query Genome, Reference Genome, ANI Value, Count of Bidirectional Fragment Mappings, and Total Query Fragments.
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90
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91 Output table looks as such:
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92
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93 +------------+------------+-----------+--------+--------+
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94 | Genome A | Genome C | 97.5883 | 1405 | 1594 |
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95 +------------+------------+-----------+--------+--------+
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96 | Genome A | Genome D | 95.6663 | 1405 | 1594 |
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97 +------------+------------+-----------+--------+--------+
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98 | Genome B | Genome C | 92.4281 | 1409 | 1553 |
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99 +------------+------------+-----------+--------+--------+
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100 | Genome B | Genome D | 99.9242 | 1396 | 1553 |
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101 +------------+------------+-----------+--------+--------+
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102
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103 |
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104 | Thanks to Thanh Lê for building the initial Galaxy wrapper.
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105 ]]></help>
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106 <expand macro="citations" />
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107 </tool>