|
0
|
1 <tool id="antismash" name="Secondary Metabolites" version="2.0.2.0">
|
|
4
|
2 <description>and Antibiotics Analysis (antiSMASH)</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.0">hmmer</requirement>
|
|
|
5 <requirement type="package" version="2.3.2">hmmer</requirement>
|
|
|
6 <requirement type="package" version="2.2.28">blast+</requirement>
|
|
|
7 <requirement type="package" version="3.8.31">muscle</requirement>
|
|
5
|
8 <requirement type="package" version="2.0.2">antismash_python_deps</requirement>
|
|
4
|
9 <requirement type="package" version="2.0.2">antismash</requirement>
|
|
|
10 </requirements>
|
|
|
11 <command>
|
|
|
12 run_antismash.py
|
|
0
|
13
|
|
4
|
14 --input $infile
|
|
|
15 --cpus 4
|
|
|
16 #set $type_list = ','.join([$type for $type in $types])
|
|
|
17 --enable $type_list
|
|
|
18 --input-type nucl
|
|
|
19 $smcogs
|
|
|
20 $clusterblast
|
|
|
21 $subclusterblast
|
|
|
22 $inclusive
|
|
|
23 $full_hmmer
|
|
|
24 $full_blast
|
|
0
|
25
|
|
4
|
26 --pfamdir $pfam_database.fields.path
|
|
0
|
27
|
|
9
|
28 ## leave out the start and end features, it can be easily replaced with Galaxy tools
|
|
|
29 ##--from START Start analysis at nucleotide specified
|
|
|
30 ##--to END
|
|
0
|
31
|
|
|
32 </command>
|
|
|
33 <inputs>
|
|
|
34 <param name="infile" type="data" format="gb,embl" label="Nucleotide sequence file in GenBank or EMBL format"/>
|
|
|
35
|
|
11
|
36 <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" truevalue="--clusterblast" falsevalue="" checked="True" />
|
|
|
37 <param name="smcogs" type="boolean" label="analysis of secondary metabolism gene families (smCOGs)"
|
|
|
38 falsevalue="" truevalue="--smcogs" checked="True" />
|
|
|
39
|
|
|
40 <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis" truevalue="--full-blast" falsevalue="" checked="False" />
|
|
|
41 <param name="subclusterblast" type="boolean" label="Subcluster Blast analysis" truevalue="--subclusterblast" falsevalue="" checked="false" />
|
|
|
42 <param name="full_hmmer" type="boolean" label="Run a whole-genome Pfam analysis" truevalue="--full-hmmer" falsevalue="" checked="false" />
|
|
0
|
43
|
|
|
44 <param name="inclusive" type="boolean" label="Use inclusive algorithm for cluster detection" truevalue="--inclusive" falsevalue="" checked="false" />
|
|
|
45
|
|
9
|
46 <param name="pfam_database" type="select" label="Pfam database" help="Pfam Covariance models">
|
|
4
|
47 <options from_file="antismash.loc">
|
|
|
48 <column name="value" index="0"/>
|
|
|
49 <column name="name" index="1"/>
|
|
|
50 <column name="path" index="2"/>
|
|
|
51 </options>
|
|
|
52 </param>
|
|
|
53
|
|
0
|
54 <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
|
|
9
|
55 <option value="t1pks" selected="True">type I polyketide synthases</option>
|
|
|
56 <option value="t2pks" selected="True">type II polyketide synthases</option>
|
|
|
57 <option value="t3pks" selected="True">type III polyketide synthases</option>
|
|
|
58 <option value="t4pks" selected="True">type IV polyketide synthases</option>
|
|
|
59 <option value="transatpks" selected="True">trans-AT PKS</option>
|
|
|
60 <option value="nrps" selected="True">nonribosomal peptide synthetases</option>
|
|
|
61 <option value="terpene" selected="True">terpene synthases</option>
|
|
|
62 <option value="lantipeptide" selected="True">lantipeptides</option>
|
|
|
63 <option value="bacteriocin" selected="True">bacteriocins</option>
|
|
|
64 <option value="blactam" selected="True">beta-lactams</option>
|
|
|
65 <option value="amglyccycl" selected="True">aminoglycosides / aminocyclitols</option>
|
|
|
66 <option value="aminocoumarin" selected="True">aminocoumarins</option>
|
|
|
67 <option value="siderophore" selected="True">siderophores</option>
|
|
|
68 <option value="ectoine" selected="True">ectoines</option>
|
|
|
69 <option value="butyrolactone" selected="True">butyrolactones</option>
|
|
|
70 <option value="indole" selected="True">indoles</option>
|
|
|
71 <option value="nucleoside" selected="True">nucleosides</option>
|
|
|
72 <option value="phosphoglycolipid" selected="True">phosphoglycolipids</option>
|
|
|
73 <option value="oligosaccharide" selected="True">oligosaccharides</option>
|
|
|
74 <option value="furan" selected="True">furans</option>
|
|
|
75 <option value="hserlactone" selected="True">hserlactones</option>
|
|
|
76 <option value="thiopeptide" selected="True">thiopeptides</option>
|
|
|
77 <option value="phenazine" selected="True">phenazines</option>
|
|
|
78 <option value="phosphonate" selected="True">phosphonates</option>
|
|
|
79 <option value="others" selected="True">others</option>
|
|
0
|
80 </param>
|
|
|
81
|
|
|
82 </inputs>
|
|
|
83 <outputs>
|
|
|
84 <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
|
|
|
85 <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" />
|
|
|
86 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
|
|
|
87 <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
|
|
|
88 <filter>(wg_blast == True or pfam == True)</filter>
|
|
|
89 </data>
|
|
|
90 </outputs>
|
|
|
91 <help>
|
|
|
92
|
|
|
93 .. class:: infomark
|
|
|
94
|
|
|
95 **What it does**
|
|
|
96
|
|
|
97 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
|
|
|
98 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
|
|
|
99
|
|
|
100
|
|
|
101 **Input**
|
|
|
102
|
|
11
|
103 The ideal input for antiSMASH is an annotated nucleotide file in Genbank format or EMBL format. If no annotation is available,
|
|
|
104 we recommend running your sequence through an annotation pipeline like RAST are one included in Galaxy.
|
|
|
105
|
|
|
106
|
|
|
107 There are several optional analyses that may or may not be run on your sequence.
|
|
|
108 Highly recommended is the Gene Cluster Blast Comparative Analysis, which runs BlastP using each amino acid sequence from a detected gene cluster as a
|
|
|
109 query on a large database of predicted protein sequences from secondary metabolite biosynthetic gene clusters, and pools the results to identify
|
|
|
110 the gene clusters that are most homologous to the gene cluster that was detected in your query nucleotide sequence.
|
|
|
111
|
|
|
112
|
|
|
113 Also available is the analysis of secondary metabolism gene families (smCOGs).
|
|
|
114 This analysis attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene
|
|
|
115 family using profile hidden Markov models specific for the conserved sequence region characteristic of this family.
|
|
|
116 Additionally, a phylogenetic tree is constructed of each gene together with the (max. 100) sequences of the smCOG seed alignment.
|
|
|
117
|
|
|
118
|
|
|
119 For the most thorough genome analysis, we provide genome-wide PFAM HMM analysis of all genes in the genome through modules of the CLUSEAN pipeline.
|
|
|
120 Of course, some regions important to secondary metabolism may have been missed in the gene cluster identification stage
|
|
|
121 (e.g. because they represent the biosynthetic pathway of a yet unknown secondary metabolite).
|
|
|
122 Therefore, when genome-wide PFAM HMM analysis is selected, the PFAM frequencies are also used to find all genome regions in which PFAM domains typical for secondary metabolism are overrepresented.
|
|
0
|
123
|
|
|
124
|
|
|
125 **References**
|
|
|
126
|
|
|
127 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
|
|
|
128 Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466.
|
|
|
129
|
|
|
130 http://antismash.secondarymetabolites.org/help.html
|
|
|
131
|
|
|
132 </help>
|
|
|
133 </tool>
|
