|
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="1.62">biopython</requirement>
|
|
|
9 <requirement type="package" version="2.0.2">antismash_python_deps</requirement>
|
|
4
|
10 <requirement type="package" version="2.0.2">antismash</requirement>
|
|
|
11 </requirements>
|
|
|
12 <command>
|
|
|
13 run_antismash.py
|
|
0
|
14
|
|
4
|
15 --input $infile
|
|
|
16 --cpus 4
|
|
|
17 #set $type_list = ','.join([$type for $type in $types])
|
|
|
18 --enable $type_list
|
|
|
19 --input-type nucl
|
|
|
20 $smcogs
|
|
|
21 $clusterblast
|
|
|
22 $subclusterblast
|
|
|
23 $inclusive
|
|
|
24 $full_hmmer
|
|
|
25 $full_blast
|
|
0
|
26
|
|
4
|
27 --pfamdir $pfam_database.fields.path
|
|
0
|
28
|
|
9
|
29 ## leave out the start and end features, it can be easily replaced with Galaxy tools
|
|
|
30 ##--from START Start analysis at nucleotide specified
|
|
|
31 ##--to END
|
|
0
|
32
|
|
|
33 </command>
|
|
|
34 <inputs>
|
|
|
35 <param name="infile" type="data" format="gb,embl" label="Nucleotide sequence file in GenBank or EMBL format"/>
|
|
|
36
|
|
|
37 <param name="smcogs" type="boolean" label="Look for sec.met. clusters of orthologous groups" falsevalue="" truevalue="--smcogs" checked="false" />
|
|
|
38 <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" truevalue="--clusterblast" falsevalue="" checked="false" />
|
|
|
39 <param name="subclusterblast" type="boolean" label="BLAST identified clusters against known subclusters" truevalue="--subclusterblast" falsevalue="" checked="false" />
|
|
|
40
|
|
|
41 <param name="inclusive" type="boolean" label="Use inclusive algorithm for cluster detection" truevalue="--inclusive" falsevalue="" checked="false" />
|
|
|
42 <param name="full_hmmer" type="boolean" label="Run a whole-genome HMMer analysis" truevalue="--full-hmmer" falsevalue="" checked="false" />
|
|
|
43 <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis" truevalue="--full-blast" falsevalue="" checked="false" />
|
|
|
44
|
|
9
|
45 <param name="pfam_database" type="select" label="Pfam database" help="Pfam Covariance models">
|
|
4
|
46 <options from_file="antismash.loc">
|
|
|
47 <column name="value" index="0"/>
|
|
|
48 <column name="name" index="1"/>
|
|
|
49 <column name="path" index="2"/>
|
|
|
50 </options>
|
|
|
51 </param>
|
|
|
52
|
|
0
|
53 <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
|
|
9
|
54 <option value="t1pks" selected="True">type I polyketide synthases</option>
|
|
|
55 <option value="t2pks" selected="True">type II polyketide synthases</option>
|
|
|
56 <option value="t3pks" selected="True">type III polyketide synthases</option>
|
|
|
57 <option value="t4pks" selected="True">type IV polyketide synthases</option>
|
|
|
58 <option value="transatpks" selected="True">trans-AT PKS</option>
|
|
|
59 <option value="nrps" selected="True">nonribosomal peptide synthetases</option>
|
|
|
60 <option value="terpene" selected="True">terpene synthases</option>
|
|
|
61 <option value="lantipeptide" selected="True">lantipeptides</option>
|
|
|
62 <option value="bacteriocin" selected="True">bacteriocins</option>
|
|
|
63 <option value="blactam" selected="True">beta-lactams</option>
|
|
|
64 <option value="amglyccycl" selected="True">aminoglycosides / aminocyclitols</option>
|
|
|
65 <option value="aminocoumarin" selected="True">aminocoumarins</option>
|
|
|
66 <option value="siderophore" selected="True">siderophores</option>
|
|
|
67 <option value="ectoine" selected="True">ectoines</option>
|
|
|
68 <option value="butyrolactone" selected="True">butyrolactones</option>
|
|
|
69 <option value="indole" selected="True">indoles</option>
|
|
|
70 <option value="nucleoside" selected="True">nucleosides</option>
|
|
|
71 <option value="phosphoglycolipid" selected="True">phosphoglycolipids</option>
|
|
|
72 <option value="oligosaccharide" selected="True">oligosaccharides</option>
|
|
|
73 <option value="furan" selected="True">furans</option>
|
|
|
74 <option value="hserlactone" selected="True">hserlactones</option>
|
|
|
75 <option value="thiopeptide" selected="True">thiopeptides</option>
|
|
|
76 <option value="phenazine" selected="True">phenazines</option>
|
|
|
77 <option value="phosphonate" selected="True">phosphonates</option>
|
|
|
78 <option value="others" selected="True">others</option>
|
|
0
|
79 </param>
|
|
|
80
|
|
|
81 </inputs>
|
|
|
82 <outputs>
|
|
|
83 <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
|
|
|
84 <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" />
|
|
|
85 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
|
|
|
86 <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
|
|
|
87 <filter>(wg_blast == True or pfam == True)</filter>
|
|
|
88 </data>
|
|
|
89 </outputs>
|
|
|
90 <help>
|
|
|
91
|
|
|
92 .. class:: infomark
|
|
|
93
|
|
|
94 That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported.
|
|
|
95 For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a
|
|
|
96 archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection.
|
|
|
97
|
|
|
98
|
|
|
99 **What it does**
|
|
|
100
|
|
|
101 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
|
|
|
102 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
|
|
|
103
|
|
|
104
|
|
|
105 **Input**
|
|
|
106
|
|
|
107 If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. You can created it with glimmer or glimmerHMM.
|
|
|
108
|
|
|
109
|
|
|
110 **References**
|
|
|
111
|
|
|
112 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
|
|
|
113 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.
|
|
|
114
|
|
|
115 http://antismash.secondarymetabolites.org/help.html
|
|
|
116
|
|
|
117 </help>
|
|
|
118 </tool>
|
