Mercurial > repos > thanhlv > nullarbor

annotate nullarbor.xml @ 0:f9c1aaf4f592 draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
author thanhlv
date Fri, 03 May 2019 07:16:27 -0400
parents
children c9e2a0019616
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f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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1 <tool id="nullarbor" name="nullarbor" version="@VERSION@">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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2 <description>Pipeline to generate complete public health microbiology reports from sequenced isolates</description>
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3 <macros>
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4 <import>macros.xml</import>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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5 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <expand macro="env" />
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10 <command detect_errors="exit_code"><![CDATA[
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12 nullarbor.pl
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13 --run
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14 --cpus $opt.cpus
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16 #if $opt.verbose
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17 $opt.verbose
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18 #end if
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20 --gcode $adv_opt.gcode
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22 #if $opt.trim
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23 $opt.trim
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24 #end if
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25
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26 #if str($adv_opt.mlst) != "auto"
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27 --mlst '$adv_opt.mlst'
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28 #end if
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30 #if str($adv_opt.snippy_opt) != ""
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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31 --snippy_opt $adv_opt.snippy_opt
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32 #end if
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34 #if str($adv_opt.roary_opt) != ""
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35 --roary_opt $adv_opt.roary_opt
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36 #end if
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38 #if str($adv_opt.mask) != "AUTO"
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39 --mask $adv_opt.mask
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40 #end if
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41
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42 --assembler $plugins.assembler
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43
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44 #if str($plugins.assembler-opt) != ""
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45 --assembler-opt $plugins.assembler-opt
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46 #end if
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47
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48 --treebuilder $plugins.treebuilder
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49
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50 #if str($plugins.treebuilder-opt) != ""
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51 --treebuilder-opt $plugins.treebuilder-opt
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52 #end if
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53
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54 --taxoner $plugins.taxoner
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55
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56 #if str($plugins.taxoner-opt) != ""
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57 --taxoner-opt $plugins.taxoner-opt
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58 #end if
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59
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60 --annotator $plugins.annotator
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61
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62 #if str($plugins.annotator-opt) != ""
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63 --annotator-opt $plugins.annotator-opt
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64 #end if
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65
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66 --name $name
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67 --ref $ref
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68 --input $tab_file
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69 --outdir out
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70
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71 ]]></command>
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72
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73 <inputs>
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74 <param name="tab_file" format="txt" type="data" label="Tab file generated from nullarbor_prepare" help="You need to run nullarbor_test for generating a tab file of reads before running this tool"/>
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75 <param name="ref" type="data" format="fasta" label="Reference genome " help="Reference file in FASTA or GBK format"/>
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76 <param name="name" type="text" optional="False" label="Job name" help="" />
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77
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78 <section name='opt' title = "Options">
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79 <param name="cpus" argument="--cpus" type="integer" value="8" label="CPUs" help="Maximum number of CPUs to use in total (Default: 8)" />
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80 <param name="verbose" argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" help="More screen output" />
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81 </section>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
82
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
83 <section name="adv_opt" title="Advanced Options">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
84 <param name="gcode" argument="--gcode" type="integer" value="11" label="Genetic code for prokka" help="(Default: 11)" />
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
85 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="False" label="Trim reads of adaptors" help="(Default: NO)" />
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
86 <param name="mlst" argument="--mlst" type="select" label="Force this MLST scheme" help="(Default: AUTO)">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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diff changeset
87 <option value="auto">AUTO</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
diff changeset
88 <option value="abaumannii">Acinetobacter baumannii</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
89 <option value="abaumannii_2">Acinetobacter baumannii 2</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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90 <option value="achromobacter">Achromobacter</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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91 <option value="aeromonas">Aeromonas</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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92 <option value="afumigatus">Aspergillus afumigatus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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93 <option value="aphagocytophilum">Anaplasma aphagocytophilum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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94 <option value="arcobacter">Arcobacter</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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95 <option value="bburgdorferi">Borrelia burgdorferi</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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96 <option value="bcc">Burkholderia cepacia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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97 <option value="bcereus">Bacillus cereus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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98 <option value="bhampsonii">Brachyspira hampsonii</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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99 <option value="bhenselae">Bartonella henselae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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100 <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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101 <option value="bifidobacterium">Bifidobacterium bifidobacterium</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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102 <option value="bintermedia">Brachyspira intermedia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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103 <option value="blicheniformis">Bacillus licheniformis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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104 <option value="bordetella">Bordetella pertussis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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105 <option value="borrelia">Borrelia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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106 <option value="bpilosicoli">Brachyspira pilosicoli</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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107 <option value="bpseudomallei">Burkholderia pseudomallei</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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108 <option value="brachyspira">Brachyspira</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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109 <option value="bsubtilis">Bacillus subtilis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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110 <option value="calbicans">Candida albicans</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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111 <option value="campylobacter">Campylobacter coli</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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112 <option value="campylobacter">Campylobacter jejuni</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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113 <option value="cbotulinum">Clostridium botulinum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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114 <option value="cconcisus">Campylobacter concisus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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115 <option value="cdifficile">Clostridium difficile</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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116 <option value="cdifficile">Peptoclostridium difficile</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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117 <option value="cdifficile_2">Clostridium difficile 2</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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118 <option value="cdiphtheriae">Corynebacterium diphtheriae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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119 <option value="cfetus">Campylobacter fetus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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120 <option value="cfreundii">Citrobacter freundii</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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121 <option value="cglabrata">Candida glabrata</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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122 <option value="chelveticus">Campylobacter helveticus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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123 <option value="chlamydiales">Chlamydia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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124 <option value="chyointestinalis">Campylobacter hyointestinalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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125 <option value="cinsulaenigrae">Campylobacter insulaenigrae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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126 <option value="ckrusei">Candida krusei</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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127 <option value="clanienae">Campylobacter lanienae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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128 <option value="clari">Campylobacter lari</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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129 <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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130 <option value="cneoformans">Cryptococcus neoformans</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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131 <option value="cronobacter">Cronobacter</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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132 <option value="csepticum">Clostridium septicum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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133 <option value="csinensis">Clonorchis sinensis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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134 <option value="csputorum">Campylobacter sputorum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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135 <option value="ctropicalis">Candida tropicalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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136 <option value="cupsaliensis">Campylobacter upsaliensis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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137 <option value="ecloacae">Enterobacter cloacae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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138 <option value="ecoli">Escherichia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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139 <option value="ecoli">Shigella</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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140 <option value="ecoli_2">Escherichia 2</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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141 <option value="edwardsiella">Edwardsiella tarda</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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142 <option value="efaecalis">Enterococcus faecalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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143 <option value="efaecium">Enterococcus faecium</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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144 <option value="fpsychrophilum">Flavobacterium psychrophilum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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145 <option value="haemophilus">Haemophilus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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146 <option value="hcinaedi">Helicobacter cinaedi</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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147 <option value="hinfluenzae">Haemophilus influenzae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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148 <option value="hparasuis">Haemophilus parasuis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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149 <option value="hpylori">Helicobacter pylori</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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150 <option value="hsuis">Haematopinus suis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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151 <option value="kkingae">Kingella kingae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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152 <option value="koxytoca">Klebsiella oxytoca</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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153 <option value="kpneumoniae">Klebsiella pneumoniae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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154 <option value="kseptempunctata">Kudoa septempunctata</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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155 <option value="lcasei">Lactobacillus casei</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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156 <option value="legionella">Legionella</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
157 <option value="leptospira">Leptospira</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
158 <option value="leptospira_2">Leptospira 2</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
159 <option value="leptospira_3">Leptospira 3</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
160 <option value="lmonocytogenes">Listeria monocytogenes</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
161 <option value="lsalivarius">Lactobacillus salivarius</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
162 <option value="mabscessus">Mycobacterium abscessus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
163 <option value="magalactiae">Mycoplasma agalactiae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
164 <option value="mbovis">Mycoplasma bovis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
165 <option value="mcatarrhalis">Moraxells catarrhalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
166 <option value="mhaemolytica">Mannheimia haemolytica</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
167 <option value="mhyorhinis">Mycoplasma hyorhinis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
168 <option value="mmassiliense">Mycobacterium massiliense</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
169 <option value="mplutonius">Melissococcus plutonius</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
170 <option value="neisseria">Neisseria</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
171 <option value="orhinotracheale">Ornithobacterium rhinotracheale</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
172 <option value="otsutsugamushi">Orientia tsutsugamushi</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
173 <option value="pacnes">Propionibacterium acnes</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
174 <option value="paeruginosa">Pseudomonas aeruginosa</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
175 <option value="pagglomerans">Pantoea agglomerans</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
176 <option value="pfluorescens">Pseudomonas fluorescens</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
177 <option value="pfreudenreichii">Propionibacterium freudenreichii</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
178 <option value="pgingivalis">Porphyromonas gingivalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
179 <option value="plarvae">Paenibacillus larvae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
180 <option value="pmultocida_multihost">Pasteurella multocida</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
181 <option value="pmultocida_rirdc">Pasteurella multocida</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
182 <option value="ppentosaceus">Pediococcus pentosaceus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
183 <option value="pshigelloides">Plesiomonas shigelloides</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
184 <option value="ranatipestifer">Riemerella anatipestifer</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
185 <option value="sagalactiae">Streptococcus agalactiae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
186 <option value="saureus">Staphylococcus aureus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
187 <option value="scanis">Streptococcus canis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
188 <option value="sdysgalactiae">Streptococcus dysgalactiae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
189 <option value="senterica">Salmonella enterica</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
190 <option value="sepidermidis">Staphylococcus epidermidis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
191 <option value="sgallolyticus">Streptococcus gallolyticus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
192 <option value="shaemolyticus">Staphylococcus haemolyticus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
193 <option value="shominis">Stapylococcus hominis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
194 <option value="sinorhizobium">Sinorhizobium</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
195 <option value="slugdunensis">Staphylococcus lugdunensis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
196 <option value="smaltophilia">Stenotrophomonas maltophilia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
197 <option value="soralis">Streptococcus oralis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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198 <option value="spneumoniae">Streptococcus pneumoniae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
199 <option value="spseudintermedius">Staphylococcus pseudintermedius</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
200 <option value="spyogenes">Streptococcus pyogenes</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
201 <option value="ssuis">Streptococcus suis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
202 <option value="sthermophilus">Streptococcus thermophilus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
203 <option value="sthermophilus_2">Streptococcus thermophilus 2</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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204 <option value="streptomyces">Streptomyces</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
205 <option value="suberis">Streptococcus uberis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
206 <option value="szooepidemicus">Streptococcus equi</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
207 <option value="taylorella">Taylorella</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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208 <option value="tenacibaculum">Tenacibaculum</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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209 <option value="tvaginalis">Trichomonas vaginalis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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210 <option value="vcholerae">Vibrio cholerae</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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211 <option value="vibrio">Vibrio</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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212 <option value="vparahaemolyticus">Vibrio parahaemolyticus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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213 <option value="vtapetis">Vibrio tapetis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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214 <option value="vvulnificus">Vibrio vulnificus</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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215 <option value="wolbachia">Wolbachia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
diff changeset
216 <option value="xfastidiosa">Xylella fastidiosa</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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217 <option value="yersinia">Yersinia</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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218 <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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219 <option value="yruckeri">Yersinia ruckeri</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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220 </param>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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parents:
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221
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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222 <param name="snippy_opt" argument="--snippy_opt" type="text" value="" label="Snippy options" help="Options to pass to snippy eg. '--mincov 10 --ram 32'" />
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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223 <param name="roary_opt" argument="--roary_opt" type="text" value="" label="Roary options" help="Options to pass to roary eg. '-iv 1.75 -s -cd 97'" />
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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224 <param name="mask" argument="--mask" type="text" value="AUTO" label="Mask regions (BED)" help="Mask core SNPS in these regions or 'auto'" />
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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225 </section>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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226
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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227 <section name="plugins" title="Plugins">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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228 <param name="treebuilder" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is skesa">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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229 <option value="skesa" selected="True">skesa</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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230 <option value="skesa_fast">skesa fast</option>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
parents:
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231 <option value="megahit">megahit</option>
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232 <option value="shovill">shovill</option>
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233 <option value="spades">Spades</option>
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234 </param>
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235 <param name="assembler-opt" argument="--assembler-opt" type="text" value="" label="Extra assembler options to pass" help="" />
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236 <param name="treebuilder" argument="--treebuilder" type="select" label="Tree-builder to use" help="Which tree builder would you like to use, default is iqtree_fast">
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237 <option value="fasttree">fasttree</option>
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238 <option value="iqtree">iqtree</option>
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239 <option value="iqtree_fast" selected="True">iqtree_fast</option>
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240 <option value="iqtree_slow">iqtree_slow</option>
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241 </param>
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242 <param name="treebuilder-opt" argument="--treebuilder-opt" type="text" value="" label="Extra tree-builder options to pass" help="" />
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243 <param name="taxoner" argument="--taxoner" type="select" label="Species ID tool to use" help="Which taxoner would you like to use, default is kraken">
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244 <option value="kraken" selected="True">kraken</option>
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245 <option value="centrifuge">centrifuge</option>
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246 </param>
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247 <param name="taxoner-opt" argument="--taxoner-opt" type="text" value="" label="Extra taxoner options to pass" help="" />
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248 <param name="annotator" argument="--annotator" type="select" label="Genome annotator to use" help="Which genome annotator would you like to use, default is prokka_fast">
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249 <option value="prokka_fast" selected="True">prokka_fast</option>
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250 </param>
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251 <param name="annotator-opt" argument="--annotator-opt" type="text" value="" label="Extra annotator options to pass" help="" />
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252 </section>
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253
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254 </inputs>
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255
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256 <outputs>
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257 <data name="nullarbor_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/nullarbor.log" >
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258 <filter>log</filter>
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259 </data>
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260 <data name="report" format="html" label="${tool.name} on ${on_string}: Report" from_work_dir="out/report/index.html"/>
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261 <data name="jobinfo" format="txt" label="${tool.name} on ${on_string}: jobinfo.csv" from_work_dir="out/report/jobinfo.csv"/>
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262 <data name="seqdata" format="txt" label="${tool.name} on ${on_string}: seqdata.csv" from_work_dir="out/report/seqdata.csv"/>
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263 <data name="identification" format="txt" label="${tool.name} on ${on_string}: identification.csv" from_work_dir="out/report/identification.csv"/>
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264 <data name="mlst" format="tabular" label="${tool.name} on ${on_string}: mlst.csv" from_work_dir="out/report/mlst.csv"/>
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265 <data name="resitome" format="tabular" label="${tool.name} on ${on_string}: resitome.csv" from_work_dir="out/report/resitome.csv"/>
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266 <data name="virulome" format="tabular" label="${tool.name} on ${on_string}: virulome.csv" from_work_dir="out/report/virulome.csv"/>
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267 <data name="assembly" format="txt" label="${tool.name} on ${on_string}: assembly.csv" from_work_dir="out/report/assembly.csv"/>
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268 <data name="reference" format="txt" label="${tool.name} on ${on_string}: reference.csv" from_work_dir="out/report/reference.csv"/>
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269 <data name="core" format="txt" label="${tool.name} on ${on_string}: core.csv" from_work_dir="out/report/core.csv"/>
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270 <data name="core_newick" format="txt" label="${tool.name} on ${on_string}: core.newick" from_work_dir="out/report/core.newick"/>
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271 <data name="snpdist" format="tabular" label="${tool.name} on ${on_string}: snpdist.csv" from_work_dir="out/report/snpdist.csv"/>
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272 <data name="pan" format="txt" label="${tool.name} on ${on_string}: pan.csv" from_work_dir="out/report/pan.csv"/>
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273 </outputs>
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274
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275 <tests>
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276 <test>
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277 </test>
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278 </tests>
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279
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280 <help><![CDATA[
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281 NAME
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282 nullarbor.pl 2.0.20181010
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283 SYNOPSIS
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284 Reads to reports for public health microbiology
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285 AUTHOR
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286 Torsten Seemann
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287 USAGE
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288 nullarbor.pl [options] --name NAME --ref REF.FA/GBK --input INPUT.TAB --outdir DIR
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289
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290 DOCUMENTATION
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291 https://github.com/tseemann/nullarbor
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292
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293 ]]></help>
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294
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295 <citations>
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296 <citation type="bibtex">
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297 @UNPUBLISHED{Seemann2018,
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298 author = {Seemann, Torsten},
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299 title = {Nullarbor: Pipeline to generate complete public health microbiology reports from sequenced isolates},
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300 year = {2018},
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301 url = {https://github.com/tseemann/nullarbor},
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302 }
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303 </citation>
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304 </citations>
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305
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306 </tool>