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1 <tool id="antismash" name="Secondary Metabolites" version="2.0.2.2">
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2 <description>and Antibiotics Analysis (antiSMASH)</description>
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3 <requirements>
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4 <requirement type="package" version="3.0">hmmer</requirement>
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5 <requirement type="package">hmmer</requirement>
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6 <requirement type="package" version="2.2.28">blast+</requirement>
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7 <requirement type="package">blast+</requirement>
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8 <requirement type="package" version="3.8.31">muscle</requirement>
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9 <requirement type="package">muscle</requirement>
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10 <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement>
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11 <requirement type="package">straight.plugin</requirement>
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12 <requirement type="package" version="1.62">biopython</requirement>
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13 <requirement type="package">biopython</requirement>
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14 <requirement type="package" version="1.2.6">pyquery</requirement>
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15 <requirement type="package">pyquery</requirement>
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16 <requirement type="package" version="0.1.2">helperlibs</requirement>
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17 <requirement type="package">helperlibs</requirement>
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18 <requirement type="package" version="0.9">cssselect</requirement>
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19 <requirement type="package">cssselect</requirement>
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20 <requirement type="package" version="2.0.2">antismash</requirement>
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21 <requirement type="package">antismash</requirement>
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22 <requirement type="package">glimmer</requirement>
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23 </requirements>
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24 <command>
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25 #import os, glob
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26 #set $outputfolder = $html.files_path
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27 #if str($infile.ext) == 'genbank':
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28 #set $file_extension = 'gb'
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29 #else:
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30 ## TODO add embl as input file
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31 #set $file_extension = 'gb'
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32 #end if
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33
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34 ln -s $infile #echo 'input_tempfile.' + $file_extension#;
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35 mkdir -p $outputfolder;
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36 run_antismash.py
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37 --cpus "\${GALAXY_SLOTS:-12}"
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38 --enable $types
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39 --input-type 'nucl'
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40 $smcogs
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41 $clusterblast
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42 $subclusterblast
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43 $inclusive
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44 $full_hmmer
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45 $full_blast
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46 $eukaryotic
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47
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48
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49 #if str($pfam_database) != "None":
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50 --pfamdir $pfam_database.fields.path
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51 #end if
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52
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53 ##--debug
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54
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55 --disable-embl
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56 --outputfolder $outputfolder
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57
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58 #echo 'input_tempfile.' + $file_extension#
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59
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60 ## leave out the start and end features, it can be easily replaced with Galaxy tools
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61 ##--from START Start analysis at nucleotide specified
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62 ##--to END
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63
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64 2>&1
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65
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66 ##
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67 ## shuffling files to create the correct outputs for Galaxy
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68 ##
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69
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70 ## html output
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71 ;
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72 cp #echo os.path.join($outputfolder, 'index.html')# $html 2> /dev/null
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73
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74 ## gene clusters
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75 #if 'geneclusterprots_tabular' in str($outputs).split(','):
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76 ;
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77 cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2> /dev/null
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78 #end if
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79
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80 #if 'geneclusterprots_fasta' in str($outputs).split(','):
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81 ;
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82 cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2> /dev/null
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83 #end if
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84
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85
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86 ##SVG images
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87 #if 'archive_svgs' in str($outputs).split(','):
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88 ;
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89 cd #echo os.path.join($outputfolder, 'svg')#
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90 #if $clusterblast:
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91 ;
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92 tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null
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93 #else:
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94 ;
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95 tar cfz $archive_svgs genecluster*
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96 #end if
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97 #end if
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98
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99 ##all files in a archive
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100 #if 'archive' in str($outputs).split(','):
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101 ;
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102 cd $outputfolder;
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103 tar cf $archive *.zip 2> /dev/null
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104 #end if
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105
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106 ## genbank
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107 #if 'gb' in str($outputs).split(','):
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108 ;
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109 cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2> /dev/null
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110 #end if
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111
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112 </command>
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113 <inputs>
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114 <param name="infile" type="data" format="genbank" label="Nucleotide sequence file in GenBank format"/>
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115
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116 <param name="eukaryotic" type="select" label="Origin of DNA">
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117 <option value="" selected="True">Prokaryotic</option>
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118 <option value="--eukaryotic">Eukaryotic</option>
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119 </param>
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120
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121 <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters"
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122 help="(--clusterblast)"
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123 truevalue="--clusterblast" falsevalue="" checked="True" />
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124 <param name="subclusterblast" type="boolean" label="Subcluster BLAST analysis"
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125 help="(--subclusterblast)"
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126 truevalue="--subclusterblast" falsevalue="" checked="false" />
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127 <param name="smcogs" type="boolean" label="Analysis of secondary metabolism gene families (smCOGs)"
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128 falsevalue="" truevalue="--smcogs" checked="True" />
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129
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130 <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis"
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131 help="(--full-blast)"
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132 truevalue="--full-blast" falsevalue="" checked="False" />
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133 <param name="full_hmmer" type="boolean" label="Run a whole-genome Pfam analysis"
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134 help="(--full-hmmer)"
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135 truevalue="--full-hmmer" falsevalue="" checked="false" />
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136
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137 <param name="inclusive" type="boolean" label="Use Cimermancic et al. algorithm for cluster detection"
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138 help="(--inclusive)"
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139 truevalue="--inclusive" falsevalue="" checked="false" />
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140
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141 <param name="pfam_database" type="select" optional="true" label="Pfam database" help="Pfam Covariance models">
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142 <options from_file="antismash.loc">
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143 <column name="value" index="0"/>
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144 <column name="name" index="1"/>
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145 <column name="path" index="2"/>
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146 </options>
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147 </param>
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148
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149 <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
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150 <option value="t1pks" selected="True">type I polyketide synthases</option>
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151 <option value="t2pks" selected="True">type II polyketide synthases</option>
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152 <option value="t3pks" selected="True">type III polyketide synthases</option>
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153 <option value="t4pks" selected="True">type IV polyketide synthases</option>
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154 <option value="transatpks" selected="True">trans-AT PKS</option>
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155 <option value="nrps" selected="True">nonribosomal peptide synthetases</option>
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156 <option value="terpene" selected="True">terpene synthases</option>
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157 <option value="lantipeptide" selected="True">lantipeptides</option>
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158 <option value="bacteriocin" selected="True">bacteriocins</option>
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159 <option value="blactam" selected="True">beta-lactams</option>
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160 <option value="amglyccycl" selected="True">aminoglycosides / aminocyclitols</option>
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161 <option value="aminocoumarin" selected="True">aminocoumarins</option>
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162 <option value="siderophore" selected="True">siderophores</option>
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163 <option value="ectoine" selected="True">ectoines</option>
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164 <option value="butyrolactone" selected="True">butyrolactones</option>
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165 <option value="indole" selected="True">indoles</option>
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166 <option value="nucleoside" selected="True">nucleosides</option>
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167 <option value="phosphoglycolipid" selected="True">phosphoglycolipids</option>
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168 <option value="oligosaccharide" selected="True">oligosaccharides</option>
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169 <option value="furan" selected="True">furans</option>
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170 <option value="hserlactone" selected="True">hserlactones</option>
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171 <option value="thiopeptide" selected="True">thiopeptides</option>
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172 <option value="phenazine" selected="True">phenazines</option>
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173 <option value="phosphonate" selected="True">phosphonates</option>
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174 <option value="other" selected="True">others</option>
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175 </param>
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176
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177 <param name="outputs" type="select" multiple="true" label="Additional outputs">
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178 <option value="geneclusterprots_fasta" selected="True">Gene cluster proteins (FASTA)</option>
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179 <option value="geneclusterprots_tabular">Gene cluster proteins (Tabular)</option>
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180 <option value="archive_svgs">All clusters as image (compressed)</option>
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181 <option value="archive">All files compressed</option>
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182 <option value="gb">Annotated genome (GenBank)</option>
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183 </param>
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184
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185 </inputs>
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186 <outputs>
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187 <data format="fasta" name="geneclusterprots_fasta" label="${tool.name} on ${on_string} (Gen Cluster Proteins)">
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188 <filter>'geneclusterprots_fasta' in outputs</filter>
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189 </data>
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190 <data format="tabular" name="geneclusterprots_tabular" label="${tool.name} on ${on_string} (Gen Cluster Proteins)">
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191 <filter>'geneclusterprots_tabular' in outputs</filter>
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192 </data>
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193 <data format="tar" name="archive" label="${tool.name} on ${on_string} (all files compressed)">
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194 <filter>'archive' in outputs</filter>
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195 </data>
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196 <data format="tar.gz" name="archive_svgs" label="${tool.name} on ${on_string} (SVG images)">
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197 <filter>'archive_svgs' in outputs</filter>
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198 </data>
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199 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)">
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200 <!-- html is default output at any time.
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201 <filter>'html' in outputs</filter>
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202 -->
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203 </data>
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204 <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)">
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205 <filter>'gb' in outputs</filter>
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206 </data>
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207 </outputs>
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208 <help>
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209
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210 .. class:: infomark
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211
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212 **What it does**
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213
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214 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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215 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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216
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217
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218 **Input**
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219
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220 The ideal input for antiSMASH is an annotated nucleotide file in Genbank format. If no annotation is available,
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221 we recommend running your sequence through an annotation pipeline like RAST are the one included in Galaxy.
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222
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223
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224 There are several optional analyses that may or may not be run on your sequence.
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225 Highly recommended is the Gene Cluster Blast Comparative Analysis, which runs BlastP using each amino acid sequence from a detected gene cluster as a
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226 query on a large database of predicted protein sequences from secondary metabolite biosynthetic gene clusters, and pools the results to identify
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227 the gene clusters that are most homologous to the gene cluster that was detected in your query nucleotide sequence.
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228
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229
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230 Also available is the analysis of secondary metabolism gene families (smCOGs).
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231 This analysis attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene
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232 family using profile hidden Markov models specific for the conserved sequence region characteristic of this family.
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233 Additionally, a phylogenetic tree is constructed of each gene together with the (max. 100) sequences of the smCOG seed alignment.
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234
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235
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236 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.
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237 Of course, some regions important to secondary metabolism may have been missed in the gene cluster identification stage
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238 (e.g. because they represent the biosynthetic pathway of a yet unknown secondary metabolite).
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239 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.
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240
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241
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242 **References**
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243
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244 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
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245 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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246
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247 http://antismash.secondarymetabolites.org/help.html
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248
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249
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250 Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash
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251
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252 </help>
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253 </tool>
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