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annotate mlst.xml @ 6:7eb5e58d2263 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:41:48 +0000
parents dba1639c1ba6
children 9a019e7a150a
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1 <tool id="mlst" name="MLST" version="@VERSION@">
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7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <description>Scans genomes against PubMLST schemes</description>
7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
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4 <xref type="bio.tools">mlst</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 <xml name="legacy_param">
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9 <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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10 </xml>
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11 </macros>
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12 <expand macro="requirements" />
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13 <expand macro="version_command" />
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15 <command detect_errors="aggressive"><![CDATA[
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16 #import re
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17
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18 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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19 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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20 #set $named_input_files = ''
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21 #for $input_file in $input_files
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22 ## Add single quotes around each input file identifier
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23 #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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24 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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25 #set $named_input_files = $named_input_files + ' ' + $_input_file
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26 #end for
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27
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28 mlst --nopath
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29 --threads "\${GALAXY_SLOTS:-1}"
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30 #if str($settings.advanced) == "advanced"
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31 #if str($settings.minid)
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32 --minid=$settings.minid
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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33 #end if
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34 #if str($settings.mincov)
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35 --mincov=$settings.mincov
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36 #end if
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37 #if $settings.novel
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38 --novel '${novel_alleles}'
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39 #end if
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40 #if str($settings.scheme_condition.set_scheme) == "auto"
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41 #if str($settings.scheme_condition.minscore)
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42 --minscore=$settings.scheme_condition.minscore
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43 #end if
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44 #if str($settings.scheme_condition.exclude)
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45 --exclude '${settings.scheme_condition.exclude}'
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46 #end if
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47 #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
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48 #if str($settings.scheme_condition.scheme)
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49 --scheme='${settings.scheme_condition.scheme}'
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50 #end if
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51 $settings.scheme_condition.legacy
0
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52 #end if
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53 #end if
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54 ${named_input_files}
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55 > "$report"
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56 ]]></command>
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57
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58 <inputs>
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59 <param type="data" name="input_files" format="fasta,genbank" multiple="true" />
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60 <conditional name="settings">
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61 <param name="advanced" type="select" label="Specify advanced parameters">
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62 <option value="simple" selected="true">No, use program defaults.</option>
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63 <option value="advanced">Yes, see full parameter list.</option>
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64 </param>
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65 <when value="simple">
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66 </when>
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67 <when value="advanced">
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68 <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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69 <param argument="--mincov" type="integer" label="Minimum DNA %coverage" value="10" help="Minimum DNA %coverage to report partial allele at all (default 10, must be between 0-100)" optional="true" />
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70 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
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71 <conditional name="scheme_condition">
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72 <param name="set_scheme" type="select" label="Automatically set MLST scheme">
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73 <option value="auto" selected="true">Automatic MLST scheme detection</option>
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74 <option value="list">Select from a list of MLST schemes</option>
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75 <option value="manual">Manually set MLST scheme</option>
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76 </param>
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77 <when value="auto">
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78 <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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79 <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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80 </when>
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81 <when value="list">
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82 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
4
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83 <option value="abaumannii">abaumannii</option>
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84 <option value="abaumannii_2">abaumannii_2</option>
3
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85 <option value="achromobacter">achromobacter</option>
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diff changeset
86 <option value="aeromonas">aeromonas</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
87 <option value="aphagocytophilum">aphagocytophilum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
88 <option value="arcobacter">arcobacter</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
89 <option value="bbacilliformis">bbacilliformis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
90 <option value="bcc">bcc</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
91 <option value="bcereus">bcereus</option>
3
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="bhampsonii">bhampsonii</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
93 <option value="bhenselae">bhenselae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
94 <option value="bhyodysenteriae">bhyodysenteriae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
95 <option value="bintermedia">bintermedia</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
96 <option value="blicheniformis">blicheniformis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
97 <option value="bordetella">bordetella</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
98 <option value="borrelia">borrelia</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
99 <option value="bpilosicoli">bpilosicoli</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
100 <option value="bpseudomallei">bpseudomallei</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
101 <option value="brachyspira">brachyspira</option>
3
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="brucella">brucella</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
103 <option value="bsubtilis">bsubtilis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
104 <option value="campylobacter">campylobacter</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
105 <option value="cbotulinum">cbotulinum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
106 <option value="cconcisus">cconcisus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
107 <option value="cdifficile">cdifficile</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
108 <option value="cdiphtheriae">cdiphtheriae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
109 <option value="cfetus">cfetus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
110 <option value="cfreundii">cfreundii</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
111 <option value="chelveticus">chelveticus</option>
3
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="chlamydiales">chlamydiales</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
113 <option value="chyointestinalis">chyointestinalis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
114 <option value="cinsulaenigrae">cinsulaenigrae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
115 <option value="clanienae">clanienae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
116 <option value="clari">clari</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
117 <option value="cmaltaromaticum">cmaltaromaticum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
118 <option value="cronobacter">cronobacter</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
119 <option value="csepticum">csepticum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
120 <option value="csputorum">csputorum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
121 <option value="cupsaliensis">cupsaliensis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
122 <option value="dnodosus">dnodosus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
123 <option value="ecloacae">ecloacae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
124 <option value="ecoli">ecoli</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
125 <option value="ecoli_2">ecoli_2</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
126 <option value="edwardsiella">edwardsiella</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
127 <option value="efaecalis">efaecalis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
128 <option value="efaecium">efaecium</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
129 <option value="fpsychrophilum">fpsychrophilum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
130 <option value="ganatis">ganatis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
131 <option value="hcinaedi">hcinaedi</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
132 <option value="hinfluenzae">hinfluenzae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
133 <option value="hparasuis">hparasuis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
134 <option value="hpylori">hpylori</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
135 <option value="hsuis">hsuis</option>
3
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="kaerogenes">kaerogenes</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
137 <option value="kkingae">kkingae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
138 <option value="koxytoca">koxytoca</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
139 <option value="kpneumoniae">kpneumoniae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
140 <option value="leptospira">leptospira</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
141 <option value="leptospira_2">leptospira_2</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
142 <option value="leptospira_3">leptospira_3</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
143 <option value="lmonocytogenes">lmonocytogenes</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
144 <option value="lsalivarius">lsalivarius</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
145 <option value="mabscessus">mabscessus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
146 <option value="magalactiae">magalactiae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
147 <option value="mbovis">mbovis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
148 <option value="mcanis">mcanis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
149 <option value="mcaseolyticus">mcaseolyticus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
150 <option value="mcatarrhalis">mcatarrhalis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
151 <option value="mhaemolytica">mhaemolytica</option>
3
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="mhyopneumoniae">mhyopneumoniae</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
153 <option value="mhyorhinis">mhyorhinis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
154 <option value="miowae">miowae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
155 <option value="mmassiliense">mmassiliense</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
156 <option value="mplutonius">mplutonius</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
157 <option value="mpneumoniae">mpneumoniae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
158 <option value="msynoviae">msynoviae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
159 <option value="mycobacteria">mycobacteria</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
160 <option value="neisseria">neisseria</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
161 <option value="orhinotracheale">orhinotracheale</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
162 <option value="otsutsugamushi">otsutsugamushi</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
163 <option value="pacnes">pacnes</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
164 <option value="paeruginosa">paeruginosa</option>
3
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="pdamselae">pdamselae</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
166 <option value="pfluorescens">pfluorescens</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
167 <option value="pgingivalis">pgingivalis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
168 <option value="plarvae">plarvae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
169 <option value="pmultocida_multihost">pmultocida_multihost</option>
3
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="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
171 <option value="ppentosaceus">ppentosaceus</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
172 <option value="pputida">pputida</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
173 <option value="psalmonis">psalmonis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
174 <option value="ranatipestifer">ranatipestifer</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
175 <option value="rhodococcus">rhodococcus</option>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
176 <option value="sagalactiae">sagalactiae</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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177 <option value="saureus">saureus</option>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
178 <option value="sbsec">sbsec</option>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
179 <option value="scanis">scanis</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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180 <option value="sdysgalactiae">sdysgalactiae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
181 <option value="senterica">senterica</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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182 <option value="sepidermidis">sepidermidis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
183 <option value="sgallolyticus">sgallolyticus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
184 <option value="shaemolyticus">shaemolyticus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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185 <option value="shominis">shominis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
186 <option value="sinorhizobium">sinorhizobium</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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187 <option value="slugdunensis">slugdunensis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
188 <option value="smaltophilia">smaltophilia</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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189 <option value="soralis">soralis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
190 <option value="spneumoniae">spneumoniae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
191 <option value="spseudintermedius">spseudintermedius</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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192 <option value="spyogenes">spyogenes</option>
3
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="ssuis">ssuis</option>
4
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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194 <option value="sthermophilus">sthermophilus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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195 <option value="sthermophilus_2">sthermophilus_2</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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196 <option value="streptomyces">streptomyces</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
197 <option value="suberis">suberis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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198 <option value="szooepidemicus">szooepidemicus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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199 <option value="taylorella">taylorella</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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200 <option value="tenacibaculum">tenacibaculum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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201 <option value="tpallidum">tpallidum</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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202 <option value="ureaplasma">ureaplasma</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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203 <option value="vcholerae">vcholerae</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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204 <option value="vcholerae2">vcholerae2</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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205 <option value="vibrio">vibrio</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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206 <option value="vparahaemolyticus">vparahaemolyticus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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207 <option value="vtapetis">vtapetis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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208 <option value="vvulnificus">vvulnificus</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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209 <option value="wolbachia">wolbachia</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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210 <option value="xfastidiosa">xfastidiosa</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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211 <option value="yersinia">yersinia</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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212 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
dba1639c1ba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
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213 <option value="yruckeri">yruckeri</option>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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214 </param>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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215 <expand macro="legacy_param" />
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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216 </when>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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217 <when value="manual">
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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218 <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
iuc
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219 <expand macro="legacy_param" />
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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220 </when>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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221 </conditional>
0
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iuc
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222 </when>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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223 </conditional>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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224 </inputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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225
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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226 <outputs>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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227 <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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228 <data name="novel_alleles" format="fasta" label="${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
iuc
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229 <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
iuc
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230 </data>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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231 </outputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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232
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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233 <tests>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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234 <!-- Basic test - will produce no results. -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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235 <test>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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236 <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
iuc
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237 <param name="advanced" value="simple"/>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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238 <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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239 </test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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240
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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241 <!-- Basic test - will produce results. -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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242 <test>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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243 <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
iuc
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244 <param name="advanced" value="simple"/>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
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245 <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
iuc
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246 </test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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247
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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248 <!-- Advanced test - Min DNA Coverage 100 -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
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249 <test>
3
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iuc
parents: 2
diff changeset
250 <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
iuc
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diff changeset
251 <param name="advanced" value="advanced"/>
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
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252 <param name="mincov" value="100"/>
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253 <output name="report" ftype="tabular" file="output_mincov100.txt"/>
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254 </test>
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255
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256 <!-- Advanced test - Min DNA ID 100 -->
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257 <test>
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258 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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259 <param name="advanced" value="advanced"/>
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260 <param name="minid" value="100"/>
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261 <output name="report" ftype="tabular" file="output_minid100.txt"/>
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262 </test>
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263
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264 <!-- Advanced test - Manually set MLST scheme -->
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265 <test>
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266 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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267 <param name="advanced" value="advanced"/>
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268 <param name="set_scheme" value="manual"/>
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269 <param name="scheme" value="saureus"/>
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270 <param name="legacy" value="true"/>
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271 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
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272 </test>
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273
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274 <!-- Advanced test - Set a MLST scheme from a list -->
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275 <test>
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276 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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277 <param name="advanced" value="advanced"/>
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278 <param name="set_scheme" value="list"/>
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279 <param name="scheme" value="saureus"/>
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280 <param name="legacy" value="true"/>
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281 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
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282 </test>
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283
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284 <!-- Advanced test - exclude scheme -->
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285 <test>
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286 <param name="input_files" value="MRSA0252_trimmed.fna"/>
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287 <param name="advanced" value="advanced"/>
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288 <param name="set_scheme" value="auto"/>
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289 <param name="exclude" value="saureus"/>
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290 <param name="legacy" value="false"/>
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291 <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>
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292 </test>
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293
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294 <!-- Advanced test - output novel alleles. -->
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295 <test>
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296 <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>
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297 <param name="advanced" value="advanced"/>
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298 <param name="minid" value="98"/>
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299 <param name="novel" value="true"/>
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300 <param name="set_scheme" value="manual"/>
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301 <param name="scheme" value="saureus"/>
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302 <param name="legacy" value="false"/>
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303 <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>
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304 <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>
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305 </test>
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306 </tests>
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307
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308 <help><![CDATA[
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309 **What it does**
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310
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311 Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
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312
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313 **Output**
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314
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315 MLST will produce a tab-seperated output file which contains:
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316 - the filename
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317 - the closest PubMLST scheme name
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318 - the ST (sequence type)
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319 - the allele IDs
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320
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321 **Example Output**
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322
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323 ::
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324
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325 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
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326
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327 **Without auto-detection**
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328
3
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329 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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330
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331 ::
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332
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333 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm
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334 NM003.fa neisseria 11 2 3 4 3 8 4 6
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335
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336 **Missing data**
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337
0
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338 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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339
3
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340 +--------+---------------------------------------+
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341 | Symbol | Meaning |
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342 +========+=======================================+
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343 | n | Exact intact allele |
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344 +--------+---------------------------------------+
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345 | ~n | Novel full length allele similar to n |
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346 +--------+---------------------------------------+
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347 | n? | Partial match to known allele |
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348 +--------+---------------------------------------+
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349 | n,m | Multiple alleles |
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350 +--------+---------------------------------------+
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351 | *-* | Allele missing |
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352 +--------+---------------------------------------+
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353
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354 Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.
0
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355
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356 Galaxy wrapper maintained by Simon Gladman.
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357 ]]></help>
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358
3
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359 <expand macro="citations" />
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360 </tool>