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