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annotate mlst.xml @ 3:022dc4bbc27e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
author iuc
date Mon, 15 Oct 2018 07:41:28 -0400
parents 11e1af1f7f35
children dba1639c1ba6
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022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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1 <tool id="mlst" name="MLST" version="@VERSION@">
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2 <description>Scans genomes against PubMLST schemes.</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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5
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6 <xml name="legacy_param">
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7 <param argument="--legacy" type="boolean" truevalue="--legacy" falsevalue="" checked="true" label="Include allele header" help="Include allele header row in output table (requires scheme to be set)" />
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8 </xml>
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9 </macros>
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iuc
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10 <expand macro="requirements" />
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11 <expand macro="version_command" />
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12
3
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13 <command detect_errors="aggressive"><![CDATA[
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14 #import re
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16 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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17 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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18 #set $named_input_files = ''
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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19 #for $input_file in $input_files
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20 ## Add single quotes around each input file identifier
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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21 #set $_input_file = "'{}'".format($input_file.element_identifier)
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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22 ln -s '${input_file}' ${_input_file} &&
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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23 #set $named_input_files = $named_input_files + ' ' + $_input_file
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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24 #end for
0
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25
3
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26 mlst --nopath
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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27 --threads "\${GALAXY_SLOTS:-1}"
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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28 #if str($settings.advanced) == "advanced"
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29 #if str($settings.minid)
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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30 --minid=$settings.minid
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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31 #end if
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32 #if str($settings.mincov)
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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33 --mincov=$settings.mincov
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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34 #end if
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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35 #if $settings.novel
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36 --novel '${novel_alleles}'
0
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37 #end if
3
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38 #if str($settings.scheme_condition.set_scheme) == "auto"
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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39 #if str($settings.scheme_condition.minscore)
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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40 --minscore=$settings.scheme_condition.minscore
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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41 #end if
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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42 #if str($settings.scheme_condition.exclude)
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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43 --exclude '${settings.scheme_condition.exclude}'
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44 #end if
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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45 #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
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46 #if str($settings.scheme_condition.scheme)
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47 --scheme='${settings.scheme_condition.scheme}'
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48 #end if
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49 $settings.scheme_condition.legacy
0
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50 #end if
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51 #end if
3
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52 ${named_input_files}
0
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53 > "$report"
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54 ]]></command>
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55
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56 <inputs>
3
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57 <param type="data" name="input_files" format="fasta,genbank" multiple="true" />
0
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58 <conditional name="settings">
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59 <param name="advanced" type="select" label="Specify advanced parameters">
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60 <option value="simple" selected="true">No, use program defaults.</option>
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61 <option value="advanced">Yes, see full parameter list.</option>
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62 </param>
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63 <when value="simple">
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64 </when>
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65 <when value="advanced">
3
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66 <param argument="--minid" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
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67 <param argument="--mincov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
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68 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
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69 <conditional name="scheme_condition">
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70 <param name="set_scheme" type="select" label="Automatically set MLST scheme">
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71 <option value="auto" selected="true">Automatic MLST scheme detection</option>
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72 <option value="list">Select from a list of MLST schemes</option>
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73 <option value="manual">Manually set MLST scheme</option>
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74 </param>
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75 <when value="auto">
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76 <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
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77 <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" />
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78 </when>
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79 <when value="list">
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80 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
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81 <option value="achromobacter">achromobacter</option>
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82 <option value="vvulnificus">vvulnificus</option>
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83 <option value="cglabrata">cglabrata</option>
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84 <option value="sthermophilus_2">sthermophilus_2</option>
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85 <option value="mmassiliense">mmassiliense</option>
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86 <option value="bhampsonii">bhampsonii</option>
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87 <option value="afumigatus">afumigatus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
88 <option value="ecloacae">ecloacae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
89 <option value="brucella">brucella</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
90 <option value="spseudintermedius">spseudintermedius</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
91 <option value="kpneumoniae">kpneumoniae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
92 <option value="edwardsiella">edwardsiella</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
93 <option value="chlamydiales">chlamydiales</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
94 <option value="leptospira_2">leptospira_2</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
95 <option value="neisseria">neisseria</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
96 <option value="vcholerae">vcholerae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
97 <option value="orhinotracheale">orhinotracheale</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
98 <option value="paeruginosa">paeruginosa</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
99 <option value="lsalivarius">lsalivarius</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
100 <option value="leptospira">leptospira</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
101 <option value="sepidermidis">sepidermidis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
102 <option value="mhyorhinis">mhyorhinis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
103 <option value="bcc">bcc</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
104 <option value="yruckeri">yruckeri</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
105 <option value="suberis">suberis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
106 <option value="yersinia">yersinia</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
107 <option value="taylorella">taylorella</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
108 <option value="kaerogenes">kaerogenes</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
109 <option value="xfastidiosa">xfastidiosa</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
110 <option value="bordetella">bordetella</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
111 <option value="cbotulinum">cbotulinum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
112 <option value="hpylori">hpylori</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
113 <option value="mpneumoniae">mpneumoniae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
114 <option value="sdysgalactiae">sdysgalactiae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
115 <option value="efaecium">efaecium</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
116 <option value="aphagocytophilum">aphagocytophilum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
117 <option value="ecoli_2">ecoli_2</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
118 <option value="ganatis">ganatis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
119 <option value="mhyopneumoniae">mhyopneumoniae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
120 <option value="bsubtilis">bsubtilis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
121 <option value="tenacibaculum">tenacibaculum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
122 <option value="campylobacter">campylobacter</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
123 <option value="ranatipestifer">ranatipestifer</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
124 <option value="mcaseolyticus">mcaseolyticus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
125 <option value="csputorum">csputorum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
126 <option value="csinensis">csinensis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
127 <option value="dnodosus">dnodosus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
128 <option value="koxytoca">koxytoca</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
129 <option value="soralis">soralis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
130 <option value="bcereus">bcereus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
131 <option value="wolbachia">wolbachia</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
132 <option value="saureus">saureus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
133 <option value="hcinaedi">hcinaedi</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
134 <option value="clari">clari</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
135 <option value="leptospira_3">leptospira_3</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
136 <option value="sinorhizobium">sinorhizobium</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
137 <option value="pmultocida_multihost">pmultocida_multihost</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
138 <option value="ecoli">ecoli</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
139 <option value="pdamselae">pdamselae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
140 <option value="pmultocida_rirdc">pmultocida_rirdc</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
141 <option value="bhyodysenteriae">bhyodysenteriae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
142 <option value="cupsaliensis">cupsaliensis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
143 <option value="efaecalis">efaecalis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
144 <option value="shaemolyticus">shaemolyticus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
145 <option value="rhodococcus">rhodococcus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
146 <option value="pacnes">pacnes</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
147 <option value="szooepidemicus">szooepidemicus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
148 <option value="pgingivalis">pgingivalis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
149 <option value="cfetus">cfetus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
150 <option value="bpilosicoli">bpilosicoli</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
151 <option value="kseptempunctata">kseptempunctata</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
152 <option value="streptomyces">streptomyces</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
153 <option value="smaltophilia">smaltophilia</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
154 <option value="ppentosaceus">ppentosaceus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
155 <option value="cronobacter">cronobacter</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
156 <option value="mhaemolytica">mhaemolytica</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
157 <option value="cdiphtheriae">cdiphtheriae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
158 <option value="vcholerae2">vcholerae2</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
159 <option value="chyointestinalis">chyointestinalis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
160 <option value="borrelia">borrelia</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
161 <option value="abaumannii">abaumannii</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
162 <option value="arcobacter">arcobacter</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
163 <option value="csepticum">csepticum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
164 <option value="mcanis">mcanis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
165 <option value="pfluorescens">pfluorescens</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
166 <option value="lmonocytogenes">lmonocytogenes</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
167 <option value="sgallolyticus">sgallolyticus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
168 <option value="cfreundii">cfreundii</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
169 <option value="mplutonius">mplutonius</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
170 <option value="vibrio">vibrio</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
171 <option value="bbacilliformis">bbacilliformis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
172 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
173 <option value="vparahaemolyticus">vparahaemolyticus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
174 <option value="mcatarrhalis">mcatarrhalis</option>
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iuc
parents: 2
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175 <option value="bintermedia">bintermedia</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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176 <option value="sagalactiae">sagalactiae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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177 <option value="kkingae">kkingae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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178 <option value="bpseudomallei">bpseudomallei</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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179 <option value="bhenselae">bhenselae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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180 <option value="spneumoniae">spneumoniae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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181 <option value="vtapetis">vtapetis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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182 <option value="senterica">senterica</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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183 <option value="mabscessus">mabscessus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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184 <option value="sthermophilus">sthermophilus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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185 <option value="brachyspira">brachyspira</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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186 <option value="mbovis">mbovis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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187 <option value="hsuis">hsuis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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188 <option value="spyogenes">spyogenes</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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189 <option value="cconcisus">cconcisus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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190 <option value="cmaltaromaticum">cmaltaromaticum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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191 <option value="abaumannii_2">abaumannii_2</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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192 <option value="aeromonas">aeromonas</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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193 <option value="miowae">miowae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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194 <option value="shominis">shominis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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195 <option value="otsutsugamushi">otsutsugamushi</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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196 <option value="hinfluenzae">hinfluenzae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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197 <option value="clanienae">clanienae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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198 <option value="sbsec">sbsec</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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199 <option value="scanis">scanis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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200 <option value="msynoviae">msynoviae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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201 <option value="hparasuis">hparasuis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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202 <option value="magalactiae">magalactiae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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203 <option value="chelveticus">chelveticus</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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204 <option value="fpsychrophilum">fpsychrophilum</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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205 <option value="ssuis">ssuis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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206 <option value="cdifficile">cdifficile</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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207 <option value="cinsulaenigrae">cinsulaenigrae</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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208 <option value="blicheniformis">blicheniformis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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209 <option value="slugdunensis">slugdunensis</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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210 <option value="plarvae">plarvae</option>
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211 </param>
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iuc
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212 <expand macro="legacy_param" />
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213 </when>
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214 <when value="manual">
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215 <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" />
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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216 <expand macro="legacy_param" />
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217 </when>
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218 </conditional>
0
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219 </when>
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220 </conditional>
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221 </inputs>
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222
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iuc
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223 <outputs>
3
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iuc
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224 <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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225 <data name="novel_alleles" format="fasta" label="${tool.name} on ${on_string}: novel_alleles.fasta">
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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226 <filter>settings['advanced'] == "advanced" and settings['novel']</filter>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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227 </data>
0
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228 </outputs>
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229
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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230 <tests>
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231 <!-- Basic test - will produce no results. -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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232 <test>
3
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233 <param name="input_files" value="Acetobacter.fna"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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234 <param name="advanced" value="simple"/>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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235 <output name="report" ftype="tabular" file="output_noresults.txt"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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236 </test>
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237
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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238 <!-- Basic test - will produce results. -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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239 <test>
3
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240 <param name="input_files" value="MRSA0252_trimmed.fna"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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241 <param name="advanced" value="simple"/>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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242 <output name="report" ftype="tabular" file="output_mrsa.txt"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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243 </test>
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244
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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245 <!-- Advanced test - Min DNA Coverage 100 -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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246 <test>
3
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247 <param name="input_files" value="MRSA0252_trimmed.fna"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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248 <param name="advanced" value="advanced"/>
3
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249 <param name="mincov" value="100"/>
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250 <output name="report" ftype="tabular" file="output_mincov100.txt"/>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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251 </test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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252
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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253 <!-- Advanced test - Min DNA ID 100 -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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254 <test>
3
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parents: 2
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255 <param name="input_files" value="MRSA0252_trimmed.fna"/>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
256 <param name="advanced" value="advanced"/>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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257 <param name="minid" value="100"/>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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258 <output name="report" ftype="tabular" file="output_minid100.txt"/>
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259 </test>
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260
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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261 <!-- Advanced test - Manually set MLST scheme -->
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262 <test>
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263 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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264 <param name="advanced" value="advanced"/>
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265 <param name="set_scheme" value="manual"/>
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266 <param name="scheme" value="saureus"/>
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267 <param name="legacy" value="true"/>
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268 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
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269 </test>
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270
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271 <!-- Advanced test - Set a MLST scheme from a list -->
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272 <test>
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273 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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274 <param name="advanced" value="advanced"/>
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275 <param name="set_scheme" value="list"/>
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276 <param name="scheme" value="saureus"/>
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277 <param name="legacy" value="true"/>
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278 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
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279 </test>
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280
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281 <!-- Advanced test - exclude scheme -->
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282 <test>
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283 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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284 <param name="advanced" value="advanced"/>
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285 <param name="set_scheme" value="auto"/>
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286 <param name="exclude" value="saureus"/>
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287 <param name="legacy" value="false"/>
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288 <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>
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289 </test>
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290
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291 <!-- Advanced test - output novel alleles. -->
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292 <test>
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293 <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>
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294 <param name="advanced" value="advanced"/>
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295 <param name="minid" value="98"/>
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296 <param name="novel" value="true"/>
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297 <param name="set_scheme" value="manual"/>
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298 <param name="scheme" value="saureus"/>
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299 <param name="legacy" value="false"/>
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300 <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>
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301 <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>
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302 </test>
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303 </tests>
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304
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305 <help><![CDATA[
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306 **What it does**
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307
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308 Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
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309
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310 **Output**
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311
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312 MLST will produce a tab-seperated output file which contains:
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313 - the filename
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314 - the closest PubMLST scheme name
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315 - the ST (sequence type)
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316 - the allele IDs
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317
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318 **Example Output**
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319
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320 ::
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321
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322 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
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323
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324 **Without auto-detection**
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325
3
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326 If you choose to manually set the MLST scheme, it will print a fixed tabular output with a heading containing allele names specific to that scheme (adjustable with **Include allele header**). To view a list of schemes, use the MLST List tool.
0
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327
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328 ::
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329
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330 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm
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331 NM003.fa neisseria 11 2 3 4 3 8 4 6
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332
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333 **Missing data**
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334
0
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335 MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
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336
3
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337 +--------+---------------------------------------+
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338 | Symbol | Meaning |
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339 +========+=======================================+
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340 | n | Exact intact allele |
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341 +--------+---------------------------------------+
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342 | ~n | Novel full length allele similar to n |
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343 +--------+---------------------------------------+
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344 | n? | Partial match to known allele |
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345 +--------+---------------------------------------+
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346 | n,m | Multiple alleles |
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347 +--------+---------------------------------------+
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348 | *-* | Allele missing |
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349 +--------+---------------------------------------+
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350
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351 Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.
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352
1
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353 Galaxy wrapper maintained by Simon Gladman.
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354 ]]></help>
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355
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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356 <expand macro="citations" />
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d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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357 </tool>