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1 <tool id="multi_antiSMASH" name="Secondary Metabolites" version="0.1">
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2 <description>and Antibiotics Analysis (multi antiSMASH)</description>
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3 <command interpreter="python">multi_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
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8 #if $input_opts.input_opts_selector == "fasta":
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9 --input $infile
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10 --glimmer_prediction $glimmer_prediction
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11 #else:
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12 --input $infile
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13 #end if
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14
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15 --input_format $input_opts.input_opts_selector
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16
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17 $eukaryotic
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18 $genecluster
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19 $smCOG
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20 $wg_blast
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21 --geneclustertypes $geneclustertypes
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22 --geneclusterprots $geneclusterprots
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23 --geneclusterprots_gff $geneclusterprots_gff
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24 --embl_path $embl
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25 > /dev/null 2> /dev/null
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26 </command>
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27 <inputs>
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28
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29 <conditional name="input_opts">
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30 <param name="input_opts_selector" type="select" label="Input format">
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31 <option value="fasta" selected="True">FASTA file (not annotated)</option>
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32 <option value="genbank">GenBank file (annotated)</option>
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33 <option value="embl">embl file (annotated)</option>
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34 </param>
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35 <when value="fasta">
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36 <param name="infile" type="data" format="fasta" label="Sequence File"/>
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37 <param name="glimmer_prediction" type="data" format="tabular" label="Glimmer Prediction File"/>
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38 </when>
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39 <when value="embl">
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40 <param name="infile" type="data" format="embl" label="embl Sequence File"/>
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41 </when>
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42 <when value="genbank">
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43 <param name="infile" type="data" format="embl" label="GenBank Sequence File"/>
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44 </when>
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45 </conditional>
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46
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47
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48
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49
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50 <param name="eukaryotic" type="boolean" label="is the DNA of Eukaryotic origin" truevalue="--eukaryotic" falsevalue="" checked="false" />
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51 <param name="smCOG" type="boolean" label="smCOG analysis for functional prediction and phylogenetic analysis of genes" falsevalue="" truevalue="--smcogs" checked="true" />
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52 <param name="genecluster" type="boolean" label="Gene Cluster Blast Comparative Analysis" truevalue="--clusterblast" falsevalue="" checked="true" />
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53 <param name="wg_blast" type="boolean" label="Whole genome BLAST results in EMBL output" truevalue="--fullblast" falsevalue="" checked="true" />
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54 <param name="pfam" type="boolean" label="Whole genome PFAM results in EMBL output" truevalue="--fullhmm" falsevalue="" checked="true" />
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55
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56 <param name="geneclustertypes" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
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57 <option value="1" selected="True">all</option>
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58 <option value="2">type I polyketide synthases</option>
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59 <option value="3">type II polyketide synthases</option>
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60 <option value="4">type III polyketide synthases</option>
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61 <option value="5">nonribosomal peptide synthetases</option>
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62 <option value="6">terpene synthases</option>
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63 <option value="7">lantibiotics</option>
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64 <option value="8">bacteriocins</option>
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65 <option value="9">beta-lactams</option>
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66 <option value="10">aminoglycosides / aminocyclitols</option>
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67 <option value="11">aminocoumarins</option>
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68 <option value="12">siderophores</option>
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69 <option value="13">ectoines</option>
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70 <option value="14">butyrolactones</option>
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71 <option value="15">indoles</option>
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72 <option value="16">nucleosides</option>
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73 <option value="17">phosphoglycolipids</option>
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74 <option value="18">melanins</option>
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75 <option value="19">others</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
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80 <data format="gff3" name="geneclusterprots_gff" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
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81 <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
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82 </data>
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83 </outputs>
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84 <help>
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85
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86 .. class:: infomark
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87
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88 That version of antiSMASH can only handle multiple sequence files.
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89 It will run antiSMASH automatically on each sequence and aggregate the most important information from all runs.
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90 It will not provide an interactive HTML output file. If you need that please use the normal antiSMASH version on a single sequence.
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91
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92
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93 .. class:: warningmark
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94
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95 **Warning on FASTA Header**
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96
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97 The FASTA header should not contain any special letters, like '|'. Please replace them with the 'sed-tool'.
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98
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99
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100 **What it does**
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101
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102 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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103 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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104
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105
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106 **Input**
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107
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108 If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. Created with glimmer or glimmerHMM.
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109
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110
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111 **References**
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112
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113 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
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114 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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115
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116 http://antismash.secondarymetabolites.org/help.html
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117
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118 </help>
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119 </tool>
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