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annotate prokka.xml @ 8:392255fa7ab9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
author iuc
date Fri, 28 Oct 2016 13:03:19 -0400
parents f5e44aad6498
children fd4b2f03cfc6
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8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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1 <tool id="prokka" name="Prokka" version="1.11.1">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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2 <description>prokaryotic genome annotation</description>
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3 <requirements>
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4 <requirement type="package" version="1.11">prokka</requirement>
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5 </requirements>
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6 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <version_command>prokka --version</version_command>
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11 <command><![CDATA[
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12 prokka
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13 --cpus \${GALAXY_SLOTS:-8}
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14 --quiet ## to avoid non-error messages written to stderr
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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15 --outdir outdir --prefix prokka ## used in outputs section
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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16 #if $locustag
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17 --locustag '$locustag'
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18 #end if
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19 #if str($increment)
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20 --increment $increment
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21 #end if
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22 --gffver $gffver
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23 #if $compliant.compliant_select == "no"
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24 #if $compliant.addgenes
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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25 --addgenes
0
95505a9fa26f Uploaded
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26 #end if
8
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27 #if str($compliant.mincontig)
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28 --mincontig $compliant.mincontig
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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29 #end if
8
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30 #else
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31 --compliant
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32 #end if
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33 #if $centre
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34 --centre '$centre'
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35 #end if
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36 #if $genus
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37 --genus '$genus'
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38 #end if
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39 #if $species
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40 --species '$species'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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41 #end if
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42 #if $strain
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43 --strain '$strain'
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44 #end if
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45 #if $plasmid
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46 --plasmid '$plasmid'
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47 #end if
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48 --kingdom $kingdom.kingdom_select
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49 #if str($kingdom.gcode)
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50 --gcode $kingdom.gcode
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51 #end if
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52 #if $usegenus
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53 --usegenus
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54 #end if
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55 #if $proteins
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56 --proteins '$proteins'
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57 #end if
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58 #if $metagenome
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59 --metagenome
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60 #end if
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61 #if $fast
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62 --fast
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63 #end if
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64 #if str($evalue)
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65 --evalue $evalue
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66 #end if
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67 #if $rfam
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68 --rfam
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69 #end if
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70 #if $norrna
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71 --norrna
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72 #end if
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73 #if $notrna
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74 --notrna
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75 #end if
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76 $input
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77 ]]></command>
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78 <inputs>
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79 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
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80 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
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81 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
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82 <param name="gffver" type="select" label="GFF version (--gffver)">
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83 <option value="3">3</option>
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84 <option value="2">2</option>
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85 <option value="1">1</option>
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86 </param>
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87 <conditional name="compliant">
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88 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
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89 <option value="no">No</option>
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90 <option value="yes">Yes</option>
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91 </param>
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92 <when value="no">
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93 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
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94 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
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95 </when>
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96 <when value="yes" />
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97 </conditional>
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98 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
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99 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
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100 <param name="species" type="text" value="" label="Species name (--species)" />
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101 <param name="strain" type="text" value="" label="Strain name (--strain)" />
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102 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
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103 <conditional name="kingdom">
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104 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
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105 <option value="Archaea">Archaea</option>
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106 <option value="Bacteria" selected="true">Bacteria</option>
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107 <option value="Viruses">Viruses</option>
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108 </param>
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109 <when value="Archaea">
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110 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
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111 </when>
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112 <when value="Bacteria">
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113 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
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114 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
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115 <option selected="true" value="none">N/A</option>
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116 <option value="pos">positive</option>
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117 <option value="neg">negative</option>
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118 </param> SignalP is not FOSS -->
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119 </when>
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120 <when value="Viruses">
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121 <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
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122 </when>
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123 </conditional>
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124 <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
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125 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
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126 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
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127 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
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128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
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129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
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130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
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131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
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132
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133 <param name="outputs" type="select" multiple="true" label="Additional outputs">
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134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
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135 <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
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136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
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137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
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138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
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139 <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
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140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
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141 <option value="tbl" selected="True">Feature Table file</option>
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142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
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143 <option value="txt" selected="True">Statistics relating to the annotated features found</option>
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144 </param>
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145
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146 </inputs>
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147 <outputs>
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148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
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149 <filter>'gff' in outputs</filter>
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150 </data>
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151 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
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152 <filter>'gbk' in outputs</filter>
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153 </data>
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154 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
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155 <filter>'fna' in outputs</filter>
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156 </data>
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157 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
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158 <filter>'faa' in outputs</filter>
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159 </data>
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160 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
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161 <filter>'ffn' in outputs</filter>
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162 </data>
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163 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
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164 <filter>'sqn' in outputs</filter>
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165 </data>
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166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
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167 <filter>'fsa' in outputs</filter>
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168 </data>
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169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
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170 <filter>'tbl' in outputs</filter>
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171 </data>
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172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
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173 <filter>'err' in outputs</filter>
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174 </data>
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175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
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176 <filter>'txt' in outputs</filter>
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177 </data>
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178 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
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179 </outputs>
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180 <tests>
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181 <test>
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182 <param name="input" ftype="fasta" value="phiX174.fasta" />
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183 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
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184 <output name="out_gff" file="out.gff" />
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185 <output name="out_gbk" file="out.gbk" lines_diff="14" />
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186 <output name="out_fna" file="out.fna" />
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187 <output name="out_faa" file="out.faa" />
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188 <output name="out_ffn" file="out.ffn" />
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189 <output name="out_sqn" file="out.sqn" lines_diff="84" />
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190 <output name="out_fsa" file="out.fsa" />
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191 <output name="out_tbl" file="out.tbl" />
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192 <output name="out.err" file="out.err" />
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193 <output name="out_txt" file="out.txt" />
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194 <output name="out_log">
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195 <assert_contents>
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196 <has_text text="Type 'prokka --citation' for more details." />
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197 </assert_contents>
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198 </output>
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199 </test>
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200 </tests>
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201 <help><![CDATA[
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202 **What it does**
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203
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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204 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
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205
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206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
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207
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208 **Output files**
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209
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210 Prokka creates several output files:
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211
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212 gff
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213 This is the master annotation in GFF format, containing both sequences and annotations
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214 gbk
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215 This is a standard GenBank file derived from the master .gff . If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence
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216 fna
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217 Nucleotide FASTA file of the input contig sequences
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218 faa
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219 Protein FASTA file of the translated CDS sequences
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220 ffn
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221 Nucleotide FASTA file of all the annotated sequences, not just CDS
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222 sqn
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223 An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
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224 fsa
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225 Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
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226 tbl
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227 Feature Table file, used by "tbl2asn" to create the .sqn file
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228 err
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229 Unacceptable annotations - the NCBI discrepancy report
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230 log
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231 Contains all the output that Prokka produced during its run
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232 txt
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233 Statistics relating to the annotated features found
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234
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235 **License and citation**
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236
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237 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
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238
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239 .. _CRS4 Srl.: http://www.crs4.it/
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240 .. _Earlham Institute: http://earlham.ac.uk/
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241 .. _MIT license: https://opensource.org/licenses/MIT
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242
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3ad7ef0ba385 Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
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243 You can use this tool only if you agree to the license terms of: `Prokka`_.
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244
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245 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
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246 ]]></help>
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247 <citations>
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248 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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249 <citation type="doi">10.1093/bioinformatics/btu153</citation>
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250 </citations>
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251 </tool>