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annotate prokka.xml @ 12:da479161bbe4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
author iuc
date Fri, 20 Jan 2017 03:39:08 -0500
parents fd4b2f03cfc6
children a17498c603ec
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392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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1 <tool id="prokka" name="Prokka" version="1.11.1">
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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
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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13 --cpus \${GALAXY_SLOTS:-8}
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14 --quiet ## to avoid non-error messages written to stderr
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15 --outdir outdir --prefix prokka ## used in outputs section
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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 $compliant.addgenes
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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25 --addgenes
0
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26 #end if
8
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27 #if str($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'
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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" display="checkboxes" label="Additional outputs">
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134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</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 (.gbk)</option>
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136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
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137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
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138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</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. (.sqn)</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 (.fsa)</option>
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141 <option value="tbl" selected="True">Feature Table file (.tbl)</option>
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142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
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143 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</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 ${on_string}: gff" from_work_dir="outdir/prokka.gff">
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149 <filter>outputs and 'gff' in outputs</filter>
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150 </data>
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151 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
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152 <filter>outputs and 'gbk' in outputs</filter>
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153 </data>
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154 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
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155 <filter>outputs and 'fna' in outputs</filter>
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156 </data>
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157 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
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158 <filter>outputs and 'faa' in outputs</filter>
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159 </data>
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160 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
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161 <filter>outputs and 'ffn' in outputs</filter>
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162 </data>
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163 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
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164 <filter>outputs and 'sqn' in outputs</filter>
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165 </data>
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166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
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167 <filter>outputs and 'fsa' in outputs</filter>
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168 </data>
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169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
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170 <filter>outputs and 'tbl' in outputs</filter>
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171 </data>
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172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
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173 <filter>outputs and 'err' in outputs</filter>
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174 </data>
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175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
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176 <filter>outputs and 'txt' in outputs</filter>
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177 </data>
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178 <data name="out_log" format="txt" label="${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
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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, which are described in the **Additional outputs** section above.
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211
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212 **License and citation**
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213
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214 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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215
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216 .. _CRS4 Srl.: http://www.crs4.it/
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217 .. _Earlham Institute: http://earlham.ac.uk/
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218 .. _MIT license: https://opensource.org/licenses/MIT
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219
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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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220 You can use this tool only if you agree to the license terms of: `Prokka`_.
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221
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222 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
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223 ]]></help>
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224 <citations>
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225 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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226 <citation type="doi">10.1093/bioinformatics/btu153</citation>
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227 </citations>
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228 </tool>