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author bjoern-gruening
date Thu, 15 Mar 2012 05:23:03 -0400
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1 <tool id="antiSMASH" name="Secondary Metabolites" version="0.1">
2 <description>and Antibiotics Analysis (antiSMASH)</description>
3 <command interpreter="python">antiSMASH_wrapper.py
4 ## The command is a Cheetah template which allows some Python based syntax.
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6 ## ./antismash.py Tue6071_genome.fasta --geneclustertypes 1 --fullblast y --fullhmm y
7 --input $infile
8 --glimmer_prediction $glimmer_prediction
9 $eukaryotic
10 $genecluster
11 $smCOG
12 $wg_blast
13 --geneclustertypes $geneclustertypes
14 --geneclusterprots $geneclusterprots
15 --zip $zip
16 --html_file $html
17 --html_path $html.files_path
18 --embl_path $embl
19 > /dev/null 2> /dev/null
20 </command>
21 <inputs>
22 <param name="infile" type="data" format="fasta" label="Sequence File"/>
23 <param name="glimmer_prediction" type="data" format="tabular" label="Glimmer Prediction File"/>
24 <param name="eukaryotic" type="boolean" label="is the DNA of Eukaryotic origin" truevalue="--eukaryotic" falsevalue="" checked="false" />
25
26 <param name="smCOG" type="boolean" label="smCOG analysis for functional prediction and phylogenetic analysis of genes" falsevalue="" truevalue="--smcogs" checked="false" />
27 <param name="genecluster" type="boolean" label="Gene Cluster Blast Comparative Analysis" truevalue="--clusterblast" falsevalue="" checked="false" />
28 <param name="wg_blast" type="boolean" label="Whole genome BLAST results in EMBL output" truevalue="--fullblast" falsevalue="" checked="false" />
29 <param name="pfam" type="boolean" label="Whole genome PFAM results in EMBL output" truevalue="--fullhmm" falsevalue="" checked="false" />
30
31 <param name="geneclustertypes" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
32 <option value="1" selected="True">all</option>
33 <option value="2">type I polyketide synthases</option>
34 <option value="3">type II polyketide synthases</option>
35 <option value="4">type III polyketide synthases</option>
36 <option value="5">nonribosomal peptide synthetases</option>
37 <option value="6">terpene synthases</option>
38 <option value="7">lantibiotics</option>
39 <option value="8">bacteriocins</option>
40 <option value="9">beta-lactams</option>
41 <option value="10">aminoglycosides / aminocyclitols</option>
42 <option value="11">aminocoumarins</option>
43 <option value="12">siderophores</option>
44 <option value="13">ectoines</option>
45 <option value="14">butyrolactones</option>
46 <option value="15">indoles</option>
47 <option value="16">nucleosides</option>
48 <option value="17">phosphoglycolipids</option>
49 <option value="18">melanins</option>
50 <option value="19">others</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
55 <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" />
56 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
57 <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
58 <filter>(wg_blast == True or pfam == True)</filter>
59 </data>
60 </outputs>
61 <help>
62
63 .. class:: infomark
64
65 That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported.
66 For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a
67 archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection.
68
69
70 **What it does**
71
72 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
73 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
74
75
76 **Input**
77
78 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.
79
80
81 **References**
82
83 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
84 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.
85
86 http://antismash.secondarymetabolites.org/help.html
87
88 </help>
89 </tool>