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annotate antismash.xml @ 5:bc88856eddab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
author bgruening
date Tue, 05 Jul 2022 10:37:38 +0000
parents e78e25d3b4bd
children
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1 <tool id="antismash" name="Antismash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='requirements'/>
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7 <expand macro="bio_tools"/>
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8 <version_command>antismash --version</version_command>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 export PYTHONWARNINGS="ignore::FutureWarning" &&
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12
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13 #import os, glob
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14 #set $htmloutputfolder = $html.files_path
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15 #if str($infile.ext) == 'genbank':
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16 #set $file_extension = 'gb'
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17 #else:
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18 #set $file_extension = $infile.ext
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19 #end if
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20
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21 ln -s '$infile' input_tempfile.$file_extension &&
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22 #if $genefinding_gff3
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23 ln -s $genefinding_gff3 annotation.gff3 &&
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24 #end if
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26 #if $sideload.file
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27 #if $sideload.format == 'harmonize'
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28 python '$__tool_directory__/harmonize2antismash.py' '$sideload.file' sideload.json &&
bc88856eddab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
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29 #else
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30 ln -s '$sideload.file' sideload.json &&
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31 #end if
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32 #end if
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34 ## create html folder
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35 mkdir -p '$htmloutputfolder' &&
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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37 antismash
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38 --cpus "\${GALAXY_SLOTS:-12}"
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39 --taxon '${cond_taxon.taxon}'
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40 #if $genefinding_gff3
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41 --genefinding-gff3 annotation.gff3
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42 #end if
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43 --genefinding-tool $cond_taxon.genefinding_tool
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44
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45 ${cb_general}
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46 ${cb_subclusters}
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47 ${cb_knownclusters}
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48 ${smcog_trees}
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49 --tta-threshold ${tta_threshold}
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50 ${asf}
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51
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52 ${clusterhmmer}
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53 ${fullhmmer}
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54 #if $cond_taxon.taxon == 'fungi':
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55 $cond_taxon.cassis
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56 #else
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57 $cond_taxon.tigrfam
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58 #end if
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59
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60 ${cc_mibig}
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61 ${rre}
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62 --logfile $log
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63
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64 ## Advanced options
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65 --minlength $advanced_options.minlength
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66 --hmmdetection-strictness $advanced_options.hmmdetection_strictness
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67 --cb-nclusters $advanced_options.cb_nclusters
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68 --cb-min-homology-scale $advanced_options.cb_min_homology_scale
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69 --rre-cutoff $advanced_options.rre_cutoff
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70 --rre-minlength $advanced_options.rre_minlength
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71
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72 #if $sideload.file
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73 --sideload 'sideload.json'
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74 #end if
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75
1
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76 input_tempfile.$file_extension &&
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77
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78 ## copy all content to html folder
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79 cp input_tempfile/index.html '${html}' 2> /dev/null &&
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80 cp -r input_tempfile/* '${htmloutputfolder}'
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81 ]]>
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82 </command>
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83 <inputs>
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84 <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>
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85 <param argument="--genefinding-gff3" type="data" format="gff3" optional="true" label="GFF3 file" help="Specify GFF3 file to extract features from" />
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86
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87 <conditional name="cond_taxon">
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88 <param argument="--taxon" type="select" label="Taxonomic classification of input sequence" help="Source of DNA">
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89 <option value="bacteria" selected="True">Bacteria</option>
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90 <option value="fungi">Fungi</option>
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91 </param>
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92 <when value="bacteria">
4
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93 <expand macro="genefinding">
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94 <option value="prodigal" selected="True">Prodigal</option>
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95 <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>
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96 </expand>
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97 <param argument="--tigrfam" type="boolean" truevalue="--tigrfam" falsevalue="" checked="false"
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98 label="Annotate with TIGRFam" help="Annotate clusters using TIGRFam profiles. TIGRFAMs is a
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99 collection of manually curated protein families focusing primarily on prokaryotic sequences" />
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100 </when>
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101 <when value="fungi">
4
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102 <expand macro="genefinding"/>
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103 <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="false"
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104 label="Motif based prediction of SM gene cluster regions" help="Improved prediction of gene cluster borders for fungal BGCs (CASSIS)"/>
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105 </when>
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106 </conditional>
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107 <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="false"
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108 label="Full genome PFAM anotation" help="Each gene product encoded in the detected BGCs is analyzed against the PFAM database.
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109 Hits are annotated in the final Genbank/EMBL files. Also, selecting this option normally increases the runtime"/>
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110
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111 <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="false"
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112 label="PFAM anotation for only clusters" help="Run a cluster-limited HMMer analysis" />
0
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113
1
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114 <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True"
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115 label="Run active site finder analysis" help="Active sites of several highly conserved biosynthetic enzymes are detected and variations of the active sites are reported"/>
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116
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117 <param argument="--cc-mibig" type="boolean" truevalue="--cc-mibig" falsevalue="" checked="false" label="Comparison against MIBiG database" help="Run a comparison against the MIBiG database" />
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118
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119 <param argument="--cb-general" type="boolean" truevalue="--cb-general" falsevalue="" checked="false"
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120 label="BLAST identified clusters against known clusters"
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121 help="Compare identified clusters against a database of antiSMASH-predicted clusters." />
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122
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123 <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="true"
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124 label="KnowCluster BLAST analysis"
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125 help="Compare identified clusters against known gene clusters from the MIBiG database. MIBiG is a hand curated data collection of biosynthetic
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126 gene clusters, which have been experimentally characterized"/>
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127
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128 <param argument="--cb-subclusters" type="boolean" truevalue="--cb-subclusters" falsevalue="" checked="true"
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129 label="Subcluster BLAST analysis"
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130 help="The identified clusters are searched against a database containing operons involved in the biosynthesis of common secondary metabolite building
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131 blocks (e.g. the biosynthesis of non-proteinogenic amino acids)" />
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132
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133 <param argument="--pfam2go" type="boolean" truevalue="--pfam2go" falsevalue="" checked="true"
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134 label="Run Pfam to Gene Ontology mapping module" />
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135
4
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136 <param argument="--rre" type="boolean" truevalue="--rre" falsevalue="" checked="true" label="RREFinder precision mode" help="Run RREFinder precision mode on all RiPP gene clusters. Many ribosomally
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137 synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs
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138 the posttranslational modification enzymes to their substrates" />
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139
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140 <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue=""
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141 label="Analysis of secondary metabolism gene families (smCOGs)"
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142 help="It attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene family using profile hidden Markov models specific for
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143 the conserved sequence region characteristic of this family. In other words, each gene of the cluster is compared to a database of clusters of orthologous groups
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144 of proteins involved in secondary metabolism"/>
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145
4
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146 <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at"
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147 help="High-GC containing bacterial sequences contain the rare Leu-codon “TTA” as a mean for post-transcriptional regulation by limiting/controlling the amount of TTA-tNRA in the cell.
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148 This type of regulation is commonly found in secondary metabolite BGCs. This feature will annotate such TTA codons in the identified BGCs. Default: 0.65"/>
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149 <section name="advanced_options" title="Advanced options">
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150 <param argument="--minlength" type="integer" min="0" value="1000" label="Min length" help="Only process sequences larger than this value. Default: 1000" />
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151 <param argument="--hmmdetection-strictness" type="select" label="HMM detection strictness" help="Defines which level of strictness to use for HMM-based cluster detection. Default: relaxed">
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152 <option value="strict">Strict</option>
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153 <option value="relaxed" selected="true">Relaxed</option>
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154 <option value="loose">Loose</option>
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155 </param>
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156 <param argument="--cb-nclusters" type="integer" min="0" max="50" value="10" label="Number of clusters from ClusterBlast to display" help="Default: 10" />
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157 <param argument="--cb-min-homology-scale" type="float" min="0" max="1" value="0" label="ClusterBlast minimum scaling factor" help="A minimum scaling factor
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158 for the query BGC in ClusterBlast results. Default: 0" />
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159 <param argument="--rre-cutoff" type="float" min="0" max="100" value="25" label="RRE cutoff" help="Bitscore cutoff for RRE pHMM detection. Default: 25.0" />
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160 <param argument="--rre-minlength" type="integer" min="0" max="100" value="50" label="RRE minlength" help="Minimum amino acid length of RRE domains. Default: 50" />
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161 </section>
0
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162
5
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163 <section name="sideload" title="Sideloading" help="Sideloading allows you to load external datasets into AntiSMASH">
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164 <param argument="--sideload" name="file" type="data" format="json" optional="true" label="sideload json file" help="Sideload json file to add to your report" />
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165 <param name="format" type="select" label="Sideload Format">
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166 <option value="harmonize">hAMRonize summarize JSON</option>
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167 <option value="native">AntiSMASH JSON</option>
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168 </param>
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169 </section>
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170
1
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171 <param name="outputs" type="select" multiple="true" label="Outputs">
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172 <option value="html" selected="True">HTML file</option>
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173 <option value="all">All results</option>
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174 <option value="embl">EMBL files</option>
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175 <option value="gb">GenBank files</option>
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176 <option value="genecluster_tabular">Gene clusters</option>
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177 <option value="log">Log file</option>
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178 </param>
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179
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180 </inputs>
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181 <outputs>
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182 <collection type="list" name="genecluster_tabular" label="${tool.name} on ${on_string}: Gene Cluster">
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183 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="input_tempfile" ext="txt" visible="false" />
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184 <filter>'genecluster_tabular' in outputs</filter>
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185 </collection>
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186 <collection name="genbank" type="list" label="${tool.name} on ${on_string}: GenBank">
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187 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="genbank" visible="false" />
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188 <filter>'gb' in outputs or fullhmmer</filter>
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189 </collection>
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190 <collection name="embl" type="list" label="${tool.name} on ${on_string}: EMBL">
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191 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="embl" visible="false" />
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192 <filter>'embl' in outputs</filter>
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193 </collection>
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194 <collection name="archive" type="list" label="${tool.name} on ${on_string}: all files compressed">
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195 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.zip" directory="input_tempfile" ext="zip" visible="false" />
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196 <filter>'all' in outputs</filter>
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197 </collection>
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198 <data format="html" name="html" label="${tool.name} on ${on_string}: HTML report" />
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199 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file">
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200 <filter>'log' in outputs</filter>
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201 </data>
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202 </outputs>
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203 <tests>
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204 <test expect_num_outputs="1">
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205 <param name="infile" value="sequence.fasta"/>
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206 <output name="html" file="index.html"/>
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207 </test>
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208 <test expect_num_outputs="2">
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209 <param name="infile" value="sequence.gb"/>
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210 <param name="outputs" value="html,gb"/>
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211 <param name="taxon" value="fungi"/>
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212 <param name="clusterhmmer" value="true"/>
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213 <param name="fullhmmer" value="true"/>
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214 <param name="cassis" value="true"/>
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215 <param name="cb_general" value="true"/>
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216 <output_collection name="genbank" type="list">
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217 <element name="input_tempfile" file="test_02.genbank" ftype="genbank" lines_diff="2"/>
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218 </output_collection>
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219 <output name="html" file="index.2.html" ftype="html">
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220 <assert_contents>
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221 <has_text text="No results found on input"/>
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222 </assert_contents>
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223 </output>
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224 </test>
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225
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226 <test expect_num_outputs="3">
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227 <param name="infile" value="sequence_long.fasta"/>
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228 <param name="genefinding_gff3" value="annotation.gff3"/>
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229 <param name="fullhmmer" value="true"/>
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230 <param name="cc_mibig" value="true"/>
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231 <param name="pfam2go" value="true"/>
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232 <param name="rre" value="true"/>
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233 <param name="outputs" value="html,gb,log"/>
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234 <section name="advanced_options">
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235 <param name="minlength" value="1000"/>
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236 <param name="hmmdetection_strictness" value="strict"/>
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237 <param name="cb_nclusters" value="10"/>
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238 <param name="cb_min_homology_scale" value="0.1"/>
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239 <param name="rre_cutoff" value="10"/>
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240 <param name="rre_minlength" value="50"/>
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241 </section>
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242 <output_collection name="genbank" type="list">
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243 <element name="input_tempfile" file="test_03.genbank" ftype="genbank" lines_diff="2"/>
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244 </output_collection>
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245 <output name="html" file="index.3.html" ftype="html">
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246 <assert_contents>
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247 <has_text text="No results found on input"/>
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248 </assert_contents>
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249 </output>
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250 <output name="log">
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251 <assert_contents>
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252 <has_text text="antiSMASH status: SUCCESS"/>
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253 <has_text text="HMM detection using strictness: strict"/>
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254 </assert_contents>
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255 </output>
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256 </test>
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257
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258 <test expect_num_outputs="1">
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259 <param name="infile" value="sequence.fasta"/>
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260 <section name="sideload">
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261 <param name="format" value="native"/>
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262 <param name="file" value="sideload.json"/>
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263 </section>
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264 <output name="html" file="index.4.html"/>
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265 </test>
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266
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267 <test expect_num_outputs="1">
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268 <param name="infile" value="sequence.fasta"/>
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269 <section name="sideload">
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270 <param name="format" value="harmonize"/>
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271 <param name="file" value="harmonize.json"/>
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272 </section>
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273 <output name="html" file="index.5.html"/>
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274 </test>
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275 </tests>
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276 <help>
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277 <![CDATA[
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278
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279 **What it does**
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280
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281 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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282 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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283
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284 antiSMASH is powered by several open source tools: NCBI BLAST+, HMMer 3, Muscle 3, Glimmer 3, FastTree, TreeGraph 2, Indigo-depict, PySVG and JQuery SVG.
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285
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286 **Input**
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287
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288 The ideal input for antiSMASH is an annotated nucleotide file in Genbank format or EMBL format.
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289 You can either upload a GenBank/EMBL file manually, or simply enter the GenBank/RefSeq accession number of your sequence for antiSMASH to upload it.
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290 If no annotation is available, we recommend running your sequence through an annotation pipeline like RAST to obtain GBK/EMBL files with high-quality annotations.
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291
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292 Alternatively, you can provide a FASTA file containing a single sequence. antiSMASH will generate a preliminary annotation using Prodigal, and use that to run the rest of the analysis.
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293 You can also provide gene annotations in GFF3 foramt. Input files should be properly formatted.
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294 If you are creating your GBK/EMBL/FASTA file manually, be sure to do so in a plain text editor like Notepad or Emacs, and saving your files as "All files (.)", ending with the correct extension (for example ".fasta", ".gbk", or ".embl".
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295
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296 There are several optional analyses that may or may not be run on your sequence. Highly recommended is the Gene Cluster Blast Comparative Analysis, which runs BlastP using each amino acid sequence from a detected gene cluster as a query on a large database of predicted protein sequences from secondary metabolite biosynthetic gene clusters, and pools the results to identify the gene clusters that are most homologous to the gene cluster that was detected in your query nucleotide sequence.
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297 This analysis is selected by default
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298
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299 Also available is the analysis of secondary metabolism gene families (smCOGs). This analysis attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene family using profile hidden Markov models specific for the conserved sequence region characteristic of this family.
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300 Additionally, a phylogenetic tree is constructed of each gene together with the (max. 100) sequences of the smCOG seed alignment. This analysis is selected by default
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301
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302 **Ouput**
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303
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304 The output of the antiSMASH analysis pipeline is organized in an interactive HTML page with SVG graphics, and different parts of the analysis are displayed in different panels for every gene cluster
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305
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306 In the upper right, a small list of buttons offers further functionality. The house-shaped button will get you back on the antiSMASH start page.
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307 The question-mark button will get you to this help page. The exclamation-mark button leads to a page explaining about antiSMASH.
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308 The downward-pointing arrow will open a menu offering to download the complete set of results from the antiSMASH run, a summary Excel file and to the summary EMBL/GenBank output file.
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309 The EMBL/GenBank file can be viewed in a genome browser such as Artemis.
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310
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311 ]]>
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312 </help>
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313 <expand macro="citations" />
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314 </tool>