Mercurial > repos > iuc > mlst

annotate mlst.xml @ 4:1f5641a52664 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
author iuc
date Sat, 29 Dec 2018 13:30:32 -0500
parents 68cdb40ff91c
children 31812e7a1315
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
1 <tool id="mlst" name="MLST" version="@VERSION@">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
2 <description>Scans genomes against PubMLST schemes.</description>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
3 <macros>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
5
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
6 <xml name="legacy_param">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
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)" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
8 </xml>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
9 </macros>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
10 <expand macro="requirements" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
11 <expand macro="version_command" />
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
12
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
13 <command detect_errors="aggressive"><![CDATA[
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
14 #import re
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
15
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
16 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
17 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
18 #set $named_input_files = ''
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
19 #for $input_file in $input_files
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
20 ## Add single quotes around each input file identifier
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
21 #set $_input_file = "'{}'".format($input_file.element_identifier)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
22 ln -s '${input_file}' ${_input_file} &&
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
23 #set $named_input_files = $named_input_files + ' ' + $_input_file
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
24 #end for
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
25
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
26 mlst --nopath
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
27 --threads "\${GALAXY_SLOTS:-1}"
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
28 #if str($settings.advanced) == "advanced"
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
29 #if str($settings.minid)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
30 --minid=$settings.minid
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
31 #end if
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
32 #if str($settings.mincov)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
33 --mincov=$settings.mincov
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
34 #end if
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
35 #if $settings.novel
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
36 --novel '${novel_alleles}'
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
37 #end if
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
38 #if str($settings.scheme_condition.set_scheme) == "auto"
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
39 #if str($settings.scheme_condition.minscore)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
40 --minscore=$settings.scheme_condition.minscore
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
41 #end if
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
42 #if str($settings.scheme_condition.exclude)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
43 --exclude '${settings.scheme_condition.exclude}'
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
44 #end if
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
45 #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
46 #if str($settings.scheme_condition.scheme)
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
47 --scheme='${settings.scheme_condition.scheme}'
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
48 #end if
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
49 $settings.scheme_condition.legacy
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
50 #end if
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
51 #end if
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
52 ${named_input_files}
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
53 > "$report"
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
54 ]]></command>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
55
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
56 <inputs>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
57 <param type="data" name="input_files" format="fasta,genbank" multiple="true" />
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
58 <conditional name="settings">
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
59 <param name="advanced" type="select" label="Specify advanced parameters">
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
60 <option value="simple" selected="true">No, use program defaults.</option>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
61 <option value="advanced">Yes, see full parameter list.</option>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
62 </param>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
63 <when value="simple">
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
64 </when>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
65 <when value="advanced">
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
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" />
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
67 <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" />
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
68 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
69 <conditional name="scheme_condition">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
70 <param name="set_scheme" type="select" label="Automatically set MLST scheme">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
71 <option value="auto" selected="true">Automatic MLST scheme detection</option>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
72 <option value="list">Select from a list of MLST schemes</option>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
73 <option value="manual">Manually set MLST scheme</option>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
74 </param>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
75 <when value="auto">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
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" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
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" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
78 </when>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
79 <when value="list">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
80 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
81 <option value="abaumannii">abaumannii</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
82 <option value="abaumannii_2">abaumannii_2</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
83 <option value="achromobacter">achromobacter</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
84 <option value="aeromonas">aeromonas</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
85 <option value="aphagocytophilum">aphagocytophilum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
86 <option value="arcobacter">arcobacter</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
87 <option value="bbacilliformis">bbacilliformis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
88 <option value="bcc">bcc</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
89 <option value="bcereus">bcereus</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
90 <option value="bhampsonii">bhampsonii</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
91 <option value="bhenselae">bhenselae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
92 <option value="bhyodysenteriae">bhyodysenteriae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
93 <option value="bintermedia">bintermedia</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
94 <option value="blicheniformis">blicheniformis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
95 <option value="bordetella">bordetella</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
96 <option value="borrelia">borrelia</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
97 <option value="bpilosicoli">bpilosicoli</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
98 <option value="bpseudomallei">bpseudomallei</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
99 <option value="brachyspira">brachyspira</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
100 <option value="brucella">brucella</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
101 <option value="bsubtilis">bsubtilis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
102 <option value="campylobacter">campylobacter</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
103 <option value="cbotulinum">cbotulinum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
104 <option value="cconcisus">cconcisus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
105 <option value="cdifficile">cdifficile</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
106 <option value="cdiphtheriae">cdiphtheriae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
107 <option value="cfetus">cfetus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
108 <option value="cfreundii">cfreundii</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
109 <option value="chelveticus">chelveticus</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
110 <option value="chlamydiales">chlamydiales</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
111 <option value="chyointestinalis">chyointestinalis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
112 <option value="cinsulaenigrae">cinsulaenigrae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
113 <option value="clanienae">clanienae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
114 <option value="clari">clari</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
115 <option value="cmaltaromaticum">cmaltaromaticum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
116 <option value="cronobacter">cronobacter</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
117 <option value="csepticum">csepticum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
118 <option value="csputorum">csputorum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
119 <option value="cupsaliensis">cupsaliensis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
120 <option value="dnodosus">dnodosus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
121 <option value="ecloacae">ecloacae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
122 <option value="ecoli">ecoli</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
123 <option value="ecoli_2">ecoli_2</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
124 <option value="edwardsiella">edwardsiella</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
125 <option value="efaecalis">efaecalis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
126 <option value="efaecium">efaecium</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
127 <option value="fpsychrophilum">fpsychrophilum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
128 <option value="ganatis">ganatis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
129 <option value="hcinaedi">hcinaedi</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
130 <option value="hinfluenzae">hinfluenzae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
131 <option value="hparasuis">hparasuis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
132 <option value="hpylori">hpylori</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
133 <option value="hsuis">hsuis</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
134 <option value="kaerogenes">kaerogenes</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
135 <option value="kkingae">kkingae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
136 <option value="koxytoca">koxytoca</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
137 <option value="kpneumoniae">kpneumoniae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
138 <option value="leptospira">leptospira</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
139 <option value="leptospira_2">leptospira_2</option>
1f5641a52664 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_3">leptospira_3</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
141 <option value="lmonocytogenes">lmonocytogenes</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
142 <option value="lsalivarius">lsalivarius</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
143 <option value="mabscessus">mabscessus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
144 <option value="magalactiae">magalactiae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
145 <option value="mbovis">mbovis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
146 <option value="mcanis">mcanis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
147 <option value="mcaseolyticus">mcaseolyticus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
148 <option value="mcatarrhalis">mcatarrhalis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
149 <option value="mhaemolytica">mhaemolytica</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
150 <option value="mhyopneumoniae">mhyopneumoniae</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
151 <option value="mhyorhinis">mhyorhinis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
152 <option value="miowae">miowae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
153 <option value="mmassiliense">mmassiliense</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
154 <option value="mplutonius">mplutonius</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
155 <option value="mpneumoniae">mpneumoniae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
156 <option value="msynoviae">msynoviae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
157 <option value="mycobacteria">mycobacteria</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
158 <option value="neisseria">neisseria</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
159 <option value="orhinotracheale">orhinotracheale</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
160 <option value="otsutsugamushi">otsutsugamushi</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
161 <option value="pacnes">pacnes</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
162 <option value="paeruginosa">paeruginosa</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
163 <option value="pdamselae">pdamselae</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
164 <option value="pfluorescens">pfluorescens</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
165 <option value="pgingivalis">pgingivalis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
166 <option value="plarvae">plarvae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
167 <option value="pmultocida_multihost">pmultocida_multihost</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
168 <option value="pmultocida_rirdc">pmultocida_rirdc</option>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
169 <option value="ppentosaceus">ppentosaceus</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
170 <option value="pputida">pputida</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
171 <option value="psalmonis">psalmonis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
172 <option value="ranatipestifer">ranatipestifer</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
173 <option value="rhodococcus">rhodococcus</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
174 <option value="sagalactiae">sagalactiae</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
175 <option value="saureus">saureus</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
176 <option value="sbsec">sbsec</option>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
177 <option value="scanis">scanis</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
178 <option value="sdysgalactiae">sdysgalactiae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
179 <option value="senterica">senterica</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
180 <option value="sepidermidis">sepidermidis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
181 <option value="sgallolyticus">sgallolyticus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
182 <option value="shaemolyticus">shaemolyticus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
183 <option value="shominis">shominis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
184 <option value="sinorhizobium">sinorhizobium</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
185 <option value="slugdunensis">slugdunensis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
186 <option value="smaltophilia">smaltophilia</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
187 <option value="soralis">soralis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
188 <option value="spneumoniae">spneumoniae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
189 <option value="spseudintermedius">spseudintermedius</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
190 <option value="spyogenes">spyogenes</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
191 <option value="ssuis">ssuis</option>
4
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
192 <option value="sthermophilus">sthermophilus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
193 <option value="sthermophilus_2">sthermophilus_2</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
194 <option value="streptomyces">streptomyces</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
195 <option value="suberis">suberis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
196 <option value="szooepidemicus">szooepidemicus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
197 <option value="taylorella">taylorella</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
198 <option value="tenacibaculum">tenacibaculum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
199 <option value="tpallidum">tpallidum</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
200 <option value="ureaplasma">ureaplasma</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
201 <option value="vcholerae">vcholerae</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
202 <option value="vcholerae2">vcholerae2</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
203 <option value="vibrio">vibrio</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
204 <option value="vparahaemolyticus">vparahaemolyticus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
205 <option value="vtapetis">vtapetis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
206 <option value="vvulnificus">vvulnificus</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
207 <option value="wolbachia">wolbachia</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
208 <option value="xfastidiosa">xfastidiosa</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
209 <option value="yersinia">yersinia</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
210 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
1f5641a52664 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
iuc
parents: 3
diff changeset
211 <option value="yruckeri">yruckeri</option>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
212 </param>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
213 <expand macro="legacy_param" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
214 </when>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
215 <when value="manual">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
216 <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)" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
217 <expand macro="legacy_param" />
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
218 </when>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
219 </conditional>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
220 </when>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
221 </conditional>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
222 </inputs>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
223
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
224 <outputs>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
225 <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
226 <data name="novel_alleles" format="fasta" label="${tool.name} on ${on_string}: novel_alleles.fasta">
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
227 <filter>settings['advanced'] == "advanced" and settings['novel']</filter>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
228 </data>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
229 </outputs>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
230
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
231 <tests>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
232 <!-- Basic test - will produce no results. -->
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
233 <test>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
234 <param name="input_files" value="Acetobacter.fna"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
235 <param name="advanced" value="simple"/>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
236 <output name="report" ftype="tabular" file="output_noresults.txt"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
237 </test>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
238
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
239 <!-- Basic test - will produce results. -->
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
240 <test>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
241 <param name="input_files" value="MRSA0252_trimmed.fna"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
242 <param name="advanced" value="simple"/>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
243 <output name="report" ftype="tabular" file="output_mrsa.txt"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
244 </test>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
245
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
246 <!-- Advanced test - Min DNA Coverage 100 -->
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
247 <test>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
248 <param name="input_files" value="MRSA0252_trimmed.fna"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
249 <param name="advanced" value="advanced"/>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
250 <param name="mincov" value="100"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
251 <output name="report" ftype="tabular" file="output_mincov100.txt"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
252 </test>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
253
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
254 <!-- Advanced test - Min DNA ID 100 -->
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
255 <test>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
256 <param name="input_files" value="MRSA0252_trimmed.fna"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
257 <param name="advanced" value="advanced"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
258 <param name="minid" value="100"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
259 <output name="report" ftype="tabular" file="output_minid100.txt"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
260 </test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
261
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
262 <!-- Advanced test - Manually set MLST scheme -->
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
263 <test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
264 <param name="input_files" value="MRSA0252_trimmed.fna"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
265 <param name="advanced" value="advanced"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
266 <param name="set_scheme" value="manual"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
267 <param name="scheme" value="saureus"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
268 <param name="legacy" value="true"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
269 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
270 </test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
271
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
272 <!-- Advanced test - Set a MLST scheme from a list -->
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
273 <test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
274 <param name="input_files" value="MRSA0252_trimmed.fna"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
275 <param name="advanced" value="advanced"/>
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
276 <param name="set_scheme" value="list"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
277 <param name="scheme" value="saureus"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
278 <param name="legacy" value="true"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
279 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
280 </test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
281
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
282 <!-- Advanced test - exclude scheme -->
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
283 <test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
284 <param name="input_files" value="MRSA0252_trimmed.fna"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
285 <param name="advanced" value="advanced"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
286 <param name="set_scheme" value="auto"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
287 <param name="exclude" value="saureus"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
288 <param name="legacy" value="false"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
289 <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
290 </test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
291
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
292 <!-- Advanced test - output novel alleles. -->
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
293 <test>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
294 <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
295 <param name="advanced" value="advanced"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
296 <param name="minid" value="98"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
297 <param name="novel" value="true"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
298 <param name="set_scheme" value="manual"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
299 <param name="scheme" value="saureus"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
300 <param name="legacy" value="false"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
301 <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
302 <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
303 </test>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
304 </tests>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
305
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
306 <help><![CDATA[
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
307 **What it does**
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
308
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
309 Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
310
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
311 **Output**
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
312
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
313 MLST will produce a tab-seperated output file which contains:
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
314 - the filename
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
315 - the closest PubMLST scheme name
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
316 - the ST (sequence type)
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
317 - the allele IDs
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
318
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
319 **Example Output**
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
320
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
321 ::
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
322
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
323 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
324
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
325 **Without auto-detection**
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
326
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
327 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
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
328
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
329 ::
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
330
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
331 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
332 NM003.fa neisseria 11 2 3 4 3 8 4 6
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
333
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
334 **Missing data**
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
335
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
336 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:
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
337
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
338 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
339 | Symbol | Meaning |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
340 +========+=======================================+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
341 | n | Exact intact allele |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
342 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
343 | ~n | Novel full length allele similar to n |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
344 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
345 | n? | Partial match to known allele |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
346 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
347 | n,m | Multiple alleles |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
348 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
349 | *-* | Allele missing |
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
350 +--------+---------------------------------------+
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
351
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
352 Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
353
1
8e8dc9a1e3e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
354 Galaxy wrapper maintained by Simon Gladman.
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
355 ]]></help>
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
356
3
68cdb40ff91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
357 <expand macro="citations" />
0
735872ff8222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
358 </tool>