Mercurial > repos > iuc > fastani

annotate fastani.xml @ 0:696d11a69c84 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
author iuc
date Tue, 18 Feb 2020 20:58:26 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
1 <tool id="fastani" name="FastANI" version="@VERSION@">
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
2 <description> fast alignment-free computation of whole-genome Average Nucleotide Identity</description>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
3 <macros>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
5 </macros>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
6 <expand macro="requirements" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
7 <version_command>fastANI --version</version_command>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code">
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
9 <![CDATA[
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
10 #import re
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
11
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
12 ### SET UP INPUTS ###
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
13 #for $input_q in $query:
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
14 #set $file_name = re.sub('[^\w_]', '_', $input_q.element_identifier)
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
15 ln -fs '$input_q' '${file_name}_query' &&
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
16 echo '${file_name}_query' >> query.lst &&
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
17 #end for
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
18
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
19 #for $input_r in $reference:
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
20 #set $file_name = re.sub('[^\w_]', '_', $input_r.element_identifier)
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
21 ln -fs '$input_r' '${file_name}_ref' &&
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
22 echo '${file_name}_ref' >> ref.lst &&
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
23 #end for
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
24
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
25
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
26 ### COMMAND ###
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
27
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
28 fastANI --ql query.lst --rl ref.lst -o output -t "\${GALAXY_SLOTS:-1}"
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
29
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
30 ]]></command>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
31 <inputs>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
32 <param name="query" type="data" format="fasta" multiple="true" label="Query Sequence(s)"
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
33 help="Specify any number of query sequences in fasta format as input." />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
34 <param name="reference" type="data" format="fasta" multiple="true" label="Reference Sequence(s)"
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
35 help="Specify any number of reference sequences in fasta format as input." />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
36 </inputs>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
37 <outputs>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
38 <data name="output" format="tabular" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
39 </outputs>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
40 <tests>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
41 <test>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
42 <param name="query" value="E.coli_1.fasta" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
43 <param name="reference" value="S.flexneri_1.fasta" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
44 <output name="output" file="single.out" compare="sim_size" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
45 </test>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
46 <test>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
47 <param name="query" value="E.coli_1.fasta,E.coli_2.fasta" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
48 <param name="reference" value="S.flexneri_1.fasta,S.flexneri_2.fasta" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
49 <output name="output" file="multi.out" compare="sim_size" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
50 </test>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
51 </tests>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
52 <help><![CDATA[
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
53
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
54 FastANI
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
55 =======
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
56
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
57 FastANI is developed for fast alignment-free computation of whole-genome
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
58 Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
59 identity of orthologous gene pairs shared between two microbial genomes.
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
60 FastANI supports pairwise comparison of both complete and draft genome
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
61 assemblies. Its underlying procedure follows a similar workflow as described
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
62 by `Goris et al. 2007 <https://doi.org/10.1099/ijs.0.64483-0>`_. However, it avoids expensive sequence alignments and
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
63 uses `Mashmap <https://github.com/marbl/MashMap>`_ as its MinHash based sequence mapping engine to compute the
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
64 orthologous mappings and alignment identity estimates. Based on our
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
65 experiments with complete and draft genomes, its accuracy is on par with
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
66 `BLAST-based ANI solver <http://enve-omics.ce.gatech.edu/ani/>`_ and it achieves two to three orders of magnitude
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
67 speedup. Therefore, it is useful for pairwise ANI computation of large
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
68 number of genome pairs. More details about its speed, accuracy and potential
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
69 applications are described here: `"High Throughput ANI Analysis of 90K
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
70 Prokaryotic Genomes Reveals Clear Species Boundaries" <https://doi-org.uml.idm.oclc.org/10.1038/s41467-018-07641-9>`_.
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
71
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
72 Please visit the authors at: https://github.com/ParBLiSS/FastANI
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
73
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
74
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
75 Inputs
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
76 ------
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
77
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
78 **Query Sequence(s):**
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
79 Input one or more query genomes in fasta format
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
80
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
81 **Reference Sequence(s):**
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
82 Input one or more reference genomes to be compared to the query genomes
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
83
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
84
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
85 Output
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
86 ------
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
87
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
88 Tabular table output with columns: Query Genome, Reference Genome, ANI Value, Count of Bidirectional Fragment Mappings, and Total Query Fragments.
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
89
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
90 Output table looks as such:
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
91
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
92 +------------+------------+-----------+--------+--------+
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
93 | Genome A | Genome C | 97.5883 | 1405 | 1594 |
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
94 +------------+------------+-----------+--------+--------+
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
95 | Genome A | Genome D | 95.6663 | 1405 | 1594 |
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
96 +------------+------------+-----------+--------+--------+
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
97 | Genome B | Genome C | 92.4281 | 1409 | 1553 |
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
98 +------------+------------+-----------+--------+--------+
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
99 | Genome B | Genome D | 99.9242 | 1396 | 1553 |
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
100 +------------+------------+-----------+--------+--------+
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
101
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
102 |
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
103 | Thanks to Thanh Lê for building the initial Galaxy wrapper.
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
104 ]]></help>
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
105 <expand macro="citations" />
696d11a69c84 "planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
iuc
parents:
diff changeset
106 </tool>