Mercurial > repos > crs4 > prokka

annotate prokka.xml @ 19:8a22554cdde2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
author iuc
date Tue, 16 Nov 2021 18:59:22 +0000
parents d643e3b03500
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
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1 <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
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2 <description>Prokaryotic genome annotation</description>
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8a22554cdde2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
iuc
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3 <xrefs>
8a22554cdde2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
iuc
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4 <xref type="bio.tools">prokka</xref>
8a22554cdde2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
iuc
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5 </xrefs>
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
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6 <macros>
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
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7 <token name="@TOOL_VERSION@">1.14.6</token>
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8a22554cdde2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
iuc
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8 <token name="@VERSION_SUFFIX@">1</token>
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d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
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9 </macros>
8
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10 <requirements>
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d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
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11 <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
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392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
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12 </requirements>
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eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
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13
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392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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14 <version_command>prokka --version</version_command>
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eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
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15 <command detect_errors="exit_code"><![CDATA[
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16 prokka
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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17 --cpus \${GALAXY_SLOTS:-8}
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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18 --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
iuc
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19 --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
iuc
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20 #if $locustag
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21 --locustag '$locustag'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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22 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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23 #if str($increment)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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24 --increment $increment
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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25 #end if
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iuc
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26 --gffver $gffver
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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27 #if $compliant.compliant_select == "no"
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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28 #if $compliant.addgenes
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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29 --addgenes
0
95505a9fa26f Uploaded
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30 #end if
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392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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31 #if str($compliant.mincontig)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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32 --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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33 #end if
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34 #else
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35 --compliant
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36 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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37 #if $centre
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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38 --centre '$centre'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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39 #end if
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40 #if $genus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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41 --genus '$genus'
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iuc
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42 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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43 #if $species
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iuc
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44 --species '$species'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
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45 #end if
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46 #if $strain
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47 --strain '$strain'
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48 #end if
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49 #if $plasmid
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50 --plasmid '$plasmid'
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51 #end if
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52 --kingdom $kingdom.kingdom_select
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53 #if str($kingdom.gcode)
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54 --gcode $kingdom.gcode
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55 #end if
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56 #if $usegenus
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57 --usegenus
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58 #end if
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59 #if $proteins
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60 --proteins '$proteins'
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61 #end if
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62 #if $metagenome
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63 --metagenome
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64 #end if
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65 #if $fast
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66 --fast
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67 #end if
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68 #if str($evalue)
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69 --evalue $evalue
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70 #end if
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71 #if $rfam
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72 --rfam
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73 #end if
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74 #if $norrna
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75 --norrna
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76 #end if
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77 #if $notrna
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78 --notrna
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79 #end if
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80 $input
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81 ]]></command>
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82 <inputs>
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83 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
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84 <param argument="--locustag" type="text" value="" label="Locus tag prefix" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
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85 <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
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86 <param argument="--gffver" type="select" label="GFF version">
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87 <option value="3">3</option>
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88 <option value="2">2</option>
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89 <option value="1">1</option>
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90 </param>
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91 <conditional name="compliant">
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92 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance"
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93 help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)">
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94 <option value="no">No</option>
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95 <option value="yes">Yes</option>
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96 </param>
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97 <when value="no">
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98 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
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99 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
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100 </when>
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101 <when value="yes" />
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102 </conditional>
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103 <param argument="--centre" type="text" value="" label="Sequencing centre ID" />
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104 <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" />
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105 <param argument="--species" type="text" value="" label="Species name" />
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106 <param argument="--strain" type="text" value="" label="Strain name" />
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107 <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" />
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108 <conditional name="kingdom">
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109 <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)">
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110 <option value="Archaea">Archaea</option>
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111 <option value="Bacteria" selected="true">Bacteria</option>
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112 <option value="Viruses">Viruses</option>
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113 </param>
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114 <when value="Archaea">
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115 <param argument="--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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116 </when>
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117 <when value="Bacteria">
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118 <param argument="--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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119 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
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120 <option selected="true" value="none">N/A</option>
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121 <option value="pos">positive</option>
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122 <option value="neg">negative</option>
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123 </param> SignalP is not FOSS -->
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124 </when>
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125 <when value="Viruses">
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126 <param argument="--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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127 </when>
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128 </conditional>
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129 <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" />
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130 <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" />
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131 <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" />
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132 <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" />
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133 <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
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134 <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
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135 <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
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136 <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
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137
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138 <param name="outputs" type="select" multiple="true" label="Additional outputs">
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139 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
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140 <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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141 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
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142 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
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143 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
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144 <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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145 <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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146 <option value="tbl" selected="True">Feature Table file (.tbl)</option>
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147 <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option>
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148 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
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149 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
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150 </param>
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151
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152 </inputs>
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153 <outputs>
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154 <data name="out_gff" format="gff3" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
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155 <filter>outputs and 'gff' in outputs</filter>
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156 </data>
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157 <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
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158 <filter>outputs and 'gbk' in outputs</filter>
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159 </data>
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160 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
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161 <filter>outputs and 'fna' in outputs</filter>
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162 </data>
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163 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
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164 <filter>outputs and 'faa' in outputs</filter>
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165 </data>
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166 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
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167 <filter>outputs and 'ffn' in outputs</filter>
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168 </data>
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169 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
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170 <filter>outputs and 'sqn' in outputs</filter>
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171 </data>
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172 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
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173 <filter>outputs and 'fsa' in outputs</filter>
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174 </data>
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175 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
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176 <filter>outputs and 'tbl' in outputs</filter>
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177 </data>
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178 <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv">
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179 <filter>outputs and 'tsv' in outputs</filter>
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180 </data>
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181 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
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182 <filter>outputs and 'err' in outputs</filter>
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183 </data>
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184 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
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185 <filter>outputs and 'txt' in outputs</filter>
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186 </data>
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187 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
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188 </outputs>
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189 <tests>
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190 <test>
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191 <param name="input" ftype="fasta" value="phiX174.fasta" />
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192 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
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193 <output name="out_gff" file="out.gff" ftype="gff3" />
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194 <output name="out_gbk" >
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195 <assert_contents>
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196 <has_text_matching expression="LOCUS" />
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197 <has_text_matching expression="//" />
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198 </assert_contents>
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199 </output>
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200 <output name="out_fna" file="out.fna" ftype="fasta" />
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201 <output name="out_faa" file="out.faa" ftype="fasta" />
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202 <output name="out_ffn" file="out.ffn" ftype="fasta" />
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203 <output name="out_sqn" >
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204 <assert_contents>
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205 <has_text_matching expression="Seq-entry" />
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206 <has_text_matching expression="contig2" />
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207 </assert_contents>
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208 </output>
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209 <output name="out_fsa" file="out.fsa" ftype="fasta" />
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210 <output name="out_tbl" file="out.tbl" ftype="txt" />
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211 <output name="out_tsv" file="out.tsv" ftype="tabular" />
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212 <output name="out_err" file="out.err" lines_diff="14" ftype="txt" />
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213 <output name="out_txt" file="out.txt" ftype="txt" />
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214 <output name="out_log">
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215 <assert_contents>
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216 <has_text text="Type 'prokka --citation' for more details." />
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217 </assert_contents>
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218 </output>
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219 </test>
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220 </tests>
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221 <help><![CDATA[
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222 **What it does**
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223
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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224 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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225
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226 .. _Prokka: http://github.com/tseemann/prokka
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227
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228 **Output files**
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229
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230 Prokka creates several output files, which are described in the **Additional outputs** section above.
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231
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232 **License and citation**
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233
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234 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_.
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235
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236 .. _CRS4 Srl.: http://www.crs4.it/
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237 .. _Earlham Institute: http://earlham.ac.uk/
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238 .. _MIT license: https://opensource.org/licenses/MIT
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239
6
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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240 You can use this tool only if you agree to the license terms of: `Prokka`_.
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241
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242 .. _Prokka: http://github.com/tseemann/prokka
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243 ]]></help>
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244 <citations>
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245 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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246 <citation type="doi">10.1093/bioinformatics/btu153</citation>
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247 </citations>
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248 </tool>