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annotate antismash.xml @ 3:5784e268efca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
author bgruening
date Sun, 09 Aug 2020 10:15:12 -0400
parents 3f0077c88c16
children e78e25d3b4bd
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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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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="antismash" name="Antismash" version="5.1.2" profile="17.01">
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3 <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>
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4 <requirements>
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5 <requirement type="package" version="5.1.2">antismash</requirement>
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6 </requirements>
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7 <version_command>antismash --version</version_command>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 export PYTHONWARNINGS="ignore::FutureWarning" &&
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11
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12 #import os, glob
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13 #set $htmloutputfolder = $html.files_path
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14 #if str($infile.ext) == 'genbank':
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15 #set $file_extension = 'gb'
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16 #else:
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17 #set $file_extension = $infile.ext
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18 #end if
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19
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20 ln -s '$infile' input_tempfile.$file_extension &&
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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22 ## create html folder
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23 mkdir -p '$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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25 antismash
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26 --cpus "\${GALAXY_SLOTS:-12}"
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27 --taxon '${cond_taxon.taxon}'
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29 --genefinding-tool $cond_taxon.genefinding_tool
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30
3
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31 ${cb_general}
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32 ${cb_subclusters}
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33 ${cb_knownclusters}
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34 ${smcog_trees}
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35 --tta-threshold ${tta_threshold}
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36 ${asf}
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37
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38 ${extra_cluster}
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39 ${clusterhmmer}
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40 ${fullhmmer}
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41 #if $cond_taxon.taxon == 'fungi':
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42 $cond_taxon.cassis
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43 #end if
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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45 input_tempfile.$file_extension &&
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46
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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47 ## copy all content to html folder
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48 cp input_tempfile/index.html '${html}' 2> /dev/null &&
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49 cp -r input_tempfile/* '${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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51 ]]>
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52 </command>
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53 <inputs>
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54 <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>
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55
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56 <conditional name="cond_taxon">
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57 <param argument="--taxon" type="select" label="Origin of DNA">
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58 <option value="bacteria" selected="True">Bacteria</option>
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59 <option value="fungi">Fungi</option>
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60 </param>
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61 <when value="bacteria">
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62 <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"
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63 help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding">
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64 <option value="prodigal" selected="True">Prodigal</option>
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65 <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>
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66 <option value="glimmerhmm">GlimmerHMM</option>
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67 <option value="none">None</option>
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68 <option value="error">Error</option>
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69 </param>
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70 </when>
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71 <when value="fungi">
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72 <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"
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73 help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding">
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74 <option value="glimmerhmm">GlimmerHMM</option>
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75 <option value="none">None</option>
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76 <option value="error">Error</option>
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77 </param>
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78 <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="False"
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79 label="Motif based prediction of SM gene cluster regions" />
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80 </when>
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81 </conditional>
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82
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83
3
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84 <param argument="--cb-general" type="boolean" truevalue="--cb-general" falsevalue="" checked="False"
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85 label="BLAST identified clusters against known clusters"
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86 help="Compare identified clusters against a database of antiSMASH-predicted clusters." />
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87 <param argument="--cb-subclusters" type="boolean" truevalue="--cb-subclusters" falsevalue="" checked="True"
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88 label="Subcluster BLAST analysis"
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89 help="Compare identified clusters against known subclusters responsible for synthesising precursors." />
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90 <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="True"
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91 label="KnowCluster BLAST analysis"
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92 help="Compare identified clusters against known gene clusters from the MIBiG database."/>
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93 <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue=""
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94 label="Analysis of secondary metabolism gene families (smCOGs)"
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95 help="Look for sec. met. clusters of orthologous groups."/>
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96 <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True"
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97 label="Run active site finder analysus" />
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98 <param argument="-pfam2go" type="boolean" truevalue="-pfam2go" falsevalue="" checked="True"
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99 label="Run Pfam to Gene Ontology mapping module" />
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100 <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at" />
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101
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102 <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="False"
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103 label="Run a cluster-limited HMMer analysis" />
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104 <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="False"
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105 label="Run a whole-genome HMMer analysis" />
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106
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107 <param name="extra_cluster" type="select" label="Clusters">
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108 <option value="--cf-create-clusters" selected="True">Find extra clusters</option>
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109 <option value="--cf-borders-only">Only annotate borders of existing clusters</option>
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110 </param>
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111
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112 <param name="outputs" type="select" multiple="true" label="Outputs">
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113 <option value="html" selected="True">HTML file</option>
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114 <option value="all">All results</option>
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115 <option value="embl">EMBL files</option>
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116 <option value="gb">GenBank files</option>
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117 <option value="genecluster_tabular">Gene clusters</option>
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118 </param>
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119
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120 </inputs>
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121 <outputs>
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122 <collection type="list" name="genecluster_tabular" label="${tool.name} on ${on_string} (Gene Cluster)">
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123 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="input_tempfile" ext="txt" visible="false" />
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124 <filter>'genecluster_tabular' in outputs</filter>
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125 </collection>
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126 <collection name="genbank" type="list" label="${tool.name} on ${on_string} (GenBank)">
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127 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="genbank" visible="false" />
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128 <filter>'gb' in outputs</filter>
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129 </collection>
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130 <collection name="embl" type="list" label="${tool.name} on ${on_string} (EMBL)">
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131 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="embl" visible="false" />
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132 <filter>'embl' in outputs</filter>
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133 </collection>
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134 <collection name="archive" type="list" label="${tool.name} on ${on_string} (all files compressed)">
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135 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.zip" directory="input_tempfile" ext="zip" visible="false" />
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136 <filter>'all' in outputs</filter>
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137 </collection>
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138 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
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139 </outputs>
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140 <tests>
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141 <test>
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142 <param name="infile" value="sequence.fasta"/>
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143 <output name="html" file="index.html"/>
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144 </test>
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145 <test>
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146 <param name="infile" value="sequence.gb"/>
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147 <param name="outputs" value="html,gb"/>
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148 <param name="taxon" value="fungi"/>
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149 <param name="clusterhmmer" value="True"/>
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150 <param name="fullhmmer" value="True"/>
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151 <param name="extra_cluster" value="--cf-create-clusters"/>
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152 <param name="cassis" value="True"/>
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153 <param name="cb_general" value="True"/>
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154 <output_collection name="genbank" type="list">
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155 <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" />
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156 <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/>
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157 </output_collection>
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158 <output name="html" file="index.2.html"/>
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159 </test>
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160 </tests>
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161 <help>
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162 <![CDATA[
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163
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164 **What it does**
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165
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166 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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167 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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168
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169 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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170
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171 **Input**
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172
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173 The ideal input for antiSMASH is an annotated nucleotide file in Genbank format or EMBL format.
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174 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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175 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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176
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177 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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178 You can also provide gene annotations in GFF3 foramt. Input files should be properly formatted.
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179 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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180
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181 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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182 This analysis is selected by default
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183
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184 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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185 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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186
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187 **Ouput**
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188
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189 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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190
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191 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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192 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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193 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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194 The EMBL/GenBank file can be viewed in a genome browser such as Artemis.
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195
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196 ]]>
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197 </help>
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198 <citations>
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199 <citation type="doi">10.1093/nar/gkv437</citation>
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200 </citations>
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201 </tool>