annotate metamlst.xml @ 0:d1df295495a9 draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
author thanhlv
date Wed, 23 Feb 2022 10:17:46 +0000
parents
children 4d3e54bace61
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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1 <tool id="metamlst" name="metamlst" version="@VERSION@">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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2 <description> performs an in-silico Multi Locus Sequence Typing (MLST) Analysis on metagenomic samples</description>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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3 <macros>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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4 <token name="@VERSION@">1.2.2</token>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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5 </macros>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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6 <requirements>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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7 <requirement type="package" version="@VERSION@">metamlst</requirement>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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8 </requirements>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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9 <version_command>metamlst.py --version | head -n 1 | cut -f 2</version_command>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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10 <command detect_errors="exit_code"><![CDATA[
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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11 #import re
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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12 ## Link in the input files, so bowtie2 can tell their type
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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13 #set compressed="False"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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14 #set reads_are_fastq = True
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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15 #if str($library.type) == 'paired':
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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16 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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17 #set name_2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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18 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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19 #set read1 = $name_1 + '.fastq.gz'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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20 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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21 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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22 #set read1 = $name_1 + '.fastq.bz2'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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23 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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24 #else if $library.input_1.is_of_type('fasta'):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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25 #set reads_are_fastq = False
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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26 #set read1 = $name_1 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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27 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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28 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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29 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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30 ln -f -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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31
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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32 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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33 #set read2 = $name_2 + '.fastq.gz'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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34 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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35 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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36 #set read2 = $name_1 + '.fastq.bz2'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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37 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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38 #else if $library.input_2.is_of_type('fasta'):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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39 #set read2 = $name_1 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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40 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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41 #set read2 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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42 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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43 ln -f -s '${library.input_2}' ${read2} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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44 #else if str($library.type) == 'paired_collection':
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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45 #set pe_input_1 = $library.input_1.forward
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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46 #set pe_input_2 = $library.input_1.reverse
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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47 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.pe_input_1.name)) + "_1"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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48 #set name_2 = re.sub('[^\w\-\s]', '_', str($library.pe_input_2.name)) + "_2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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49 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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50 #set read1 = $name_1 + '.fastq.gz'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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51 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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52 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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53 #set read1 = $name_1 + '.fastq.bz2'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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54 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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55 #else if $library.input_1.forward.is_of_type('fasta'):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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56 #set reads_are_fastq = False
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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57 #set read1 = $name_1 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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58 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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59 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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60 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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61 ln -s '${library.input_1.forward}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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62
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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63 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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64 #set read2 = $name_2 + '.fastq.gz'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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65 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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66 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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67 #set read2 = $name_2 + '.fastq.bz2'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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68 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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69 #else if $library.input_1.reverse.is_of_type("fasta"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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70 #set read2 = $name_2 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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71 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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72 #set read2 = $name_2 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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73 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
74 ln -s '${library.input_1.reverse}' ${read2} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
75
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
76 #else if str($library.type) == 'paired_interleaved':
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
77 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
78 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
79 #set read1 = $name_1 + '.fastq.gz'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
80 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
81 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
82 #set read1 = $name_1 + '.fastq.bz2'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
83 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
84 #else if $library.input_1.is_of_type("fasta"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
85 #set reads_are_fastq = False
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
86 #set read1 = $name_1 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
87 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
88 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
89 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
90 ln -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
91 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
92 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
93 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
94 #set read1 = $name_1.fastq.gz
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
95 #set compressed = "GZ"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
96 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
97 #set read1 = $name_1.fastq.bz2
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
98 #set compressed = "BZ2"
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
99 #else if $library.input_1.is_of_type("fasta"):
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
100 #set reads_are_fastq = False
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
101 #set read1 = $name_1 + '.fasta'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
102 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
103 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
104 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
105 ln -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
106 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
107
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
108 metamlst-index.py
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
109 -i bowtie_MmetaMLST
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
110 -d '$metamlstdb.fields.path' &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
111
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
112 bowtie2
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
113 --very-sensitive-local
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
114 -a
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
115 --no-unal
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
116
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
117 ## number of threads
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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parents:
diff changeset
118 -p \${GALAXY_SLOTS:-4}
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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parents:
diff changeset
119
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
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diff changeset
120 ## index file path
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
121 -x bowtie_MmetaMLST
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
122
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
123 ## Input reads
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
124 #if str( $library.type ) == "single":
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
125 -U '${read1}'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
126 #elif str( $library.type ) == "paired_interleaved":
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
127 --interleaved '${read1}'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
128 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
129 -1 '${read1}'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
130 -2 '${read2}'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
131 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
132 | samtools view -bS -F 4 - > ${read1}.bam &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
133 metamlst.py
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
134 #if $filter_species.filter=='yes'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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parents:
diff changeset
135 #set species_list = ",".join([$species for $species in $filter_species.species])
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
136 --filter $species_list
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
137 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
138 --penalty $penalty
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
139 --minscore $minscore
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
140 --max_xM $max_xm
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
141 --min_read_len $min_read_len
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
142 --min_accuracy $min_accuracy
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
143 --nloci $nloci
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
144 $log
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
145 $write_sequences
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
146 ${read1}.bam
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
147 -o ./out
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
148 -d '$metamlstdb.fields.path' &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
149 metamlst-merge.py ./out -d '$metamlstdb.fields.path' &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
150 #if $log
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
151 cat ./out/*.out > log.txt &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
152 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
153 #if $write_sequences
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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154 cat ./out/*.nfo > sequences.txt
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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155 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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156 ]]> </command>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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157
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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158 <inputs>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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159 <conditional name="library">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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160 <param name="type" type="select" label="Is this single or paired library">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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161 <option value="single">Single-end</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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162 <option value="paired">Paired-end</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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163 <option value="paired_collection">Paired-end Dataset Collection</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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164 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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165 </param>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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166
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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167 <when value="single">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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168 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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169 </when>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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170 <when value="paired">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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171 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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172 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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173 </when>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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174 <when value="paired_collection">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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175 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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176 </when>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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177 <when value="paired_interleaved">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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178 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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179 </when>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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180 </conditional>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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181 <param name="metamlstdb" label="Select a database" type="select">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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182 <options from_data_table="metamlstdb">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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183 <validator message="No database is available" type="no_options" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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184 </options>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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185 </param>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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186 <conditional name="filter_species">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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187 <param name="filter" type="select" label="Filtering species">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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188 <option value="yes">Yes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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189 <option value="no" selected="true">No</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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190 </param>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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191 <when value="yes">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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192 <param name="species" type="select" multiple="true" label="Filter species">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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193 <option value="achromobacter">Achromobacter spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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194 <option value="abaumannii1">Acinetobacter baumannii#1</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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195 <option value="abaumannii2">Acinetobacter baumannii#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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196 <option value="aeromonas">Aeromonas spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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197 <option value="aactinomycetemcomitans">Aggregatibacter actinomycetemcomitans</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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198 <option value="aphagocytophilum">Anaplasma phagocytophilum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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199 <option value="arcobacter">Arcobacter spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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200 <option value="afumigatus">Aspergillus fumigatus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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201 <option value="bcereus">Bacillus cereus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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202 <option value="blicheniformis">Bacillus licheniformis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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203 <option value="bsubtilis">Bacillus subtilis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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204 <option value="bbacilliformis">Bartonella bacilliformis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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205 <option value="bhenselae">Bartonella henselae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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206 <option value="bwashoensis">Bartonella washoensis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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207 <option value="bordetella">Bordetella spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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208 <option value="borrelia">Borrelia spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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209 <option value="bhampsonii">Brachyspira hampsonii</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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210 <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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211 <option value="bintermedia">Brachyspira intermedia</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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212 <option value="bpilosicoli">Brachyspira pilosicoli</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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213 <option value="brachyspira">Brachyspira spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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214 <option value="brucella">Brucella spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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215 <option value="bcepacia">Burkholderia cepacia complex</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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216 <option value="bpseudomallei">Burkholderia pseudomallei</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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217 <option value="cconcisus-curvus">Campylobacter concisus/curvus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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218 <option value="cfetus">Campylobacter fetus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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219 <option value="chelveticus">Campylobacter helveticus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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220 <option value="chyointestinalis">Campylobacter hyointestinalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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221 <option value="cinsulaenigrae">Campylobacter insulaenigrae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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222 <option value="cjejuni">Campylobacter jejuni</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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223 <option value="clanienae">Campylobacter lanienae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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224 <option value="clari">Campylobacter lari</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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225 <option value="csputorum">Campylobacter sputorum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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226 <option value="cupsaliensis">Campylobacter upsaliensis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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diff changeset
227 <option value="calbicans">Candida albicans</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
228 <option value="cglabrata">Candida glabrata</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
229 <option value="ckrusei">Candida krusei</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
230 <option value="ctropicalis">Candida tropicalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
231 <option value="cliberibacter">Candidatus Liberibacter solanacearum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
232 <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
233 <option value="chlamydiales">Chlamydiales spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
234 <option value="cfreundii">Citrobacter freundii</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
235 <option value="csinensis">Clonorchis sinensis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
236 <option value="cdifficile">Clostridioides difficile</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
237 <option value="cbotulinum">Clostridium botulinum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
238 <option value="cperfringens">Clostridium perfringens</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
239 <option value="csepticum">Clostridium septicum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
240 <option value="cdiphtheriae">Corynebacterium diphtheriae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
241 <option value="cronobacter">Cronobacter spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
242 <option value="dnodosus">Dichelobacter nodosus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
243 <option value="edwardsiella">Edwardsiella spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
244 <option value="ecloacae">Enterobacter cloacae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
245 <option value="efaecalis">Enterococcus faecalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
246 <option value="efaecium">Enterococcus faecium</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
247 <option value="ecoli1">Escherichia coli#1</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
248 <option value="ecoli2">Escherichia coli#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
249 <option value="fpsychrophilum">Flavobacterium psychrophilum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
250 <option value="ganatis">Gallibacterium anatis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
251 <option value="geotrichum">Geotrichum spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
252 <option value="gparasuis">Glaesserella parasuis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
253 <option value="hinfluenzae">Haemophilus influenzae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
254 <option value="hcinaedi">Helicobacter cinaedi</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
255 <option value="hpylori">Helicobacter pylori</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
256 <option value="hsuis">Helicobacter suis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
257 <option value="kkingae">Kingella kingae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
258 <option value="kaerogenes">Klebsiella aerogenes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
259 <option value="koxytoca">Klebsiella oxytoca</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
260 <option value="kpneumoniae">Klebsiella pneumoniae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
261 <option value="kseptempunctata">Kudoa septempunctata</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
262 <option value="lsalivarius">Lactobacillus salivarius</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
263 <option value="leptospira">Leptospira spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
264 <option value="leptospira2">Leptospira spp.#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
265 <option value="leptospira3">Leptospira spp.#3</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
266 <option value="lmonocytogenes">Listeria monocytogenes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
267 <option value="mcanis">Macrococcus canis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
268 <option value="mcaseolyticus">Macrococcus caseolyticus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
269 <option value="mhaemolytica">Mannheimia haemolytica</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
270 <option value="mplutonius">Melissococcus plutonius</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
271 <option value="mcatarrhalis">Moraxella catarrhalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
272 <option value="mycobacteria">Mycobacteria spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
273 <option value="mabscessus">Mycobacterium abscessus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
274 <option value="mmassiliense">Mycobacterium massiliense</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
275 <option value="magalactiae">Mycoplasma agalactiae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
276 <option value="mbovis">Mycoplasma bovis (legacy)</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
277 <option value="mflocculare">Mycoplasma flocculare</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
278 <option value="mgallisepticum1">Mycoplasma gallisepticum#1</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
279 <option value="mgallisepticum2">Mycoplasma gallisepticum#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
280 <option value="mhominis">Mycoplasma hominis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
281 <option value="mhyopneumoniae">Mycoplasma hyopneumoniae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
282 <option value="mhyorhinis">Mycoplasma hyorhinis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
283 <option value="miowae">Mycoplasma iowae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
284 <option value="mpneumoniae">Mycoplasma pneumoniae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
285 <option value="msynoviae">Mycoplasma synoviae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
286 <option value="neisseria">Neisseria spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
287 <option value="otsutsugamushi">Orientia tsutsugamushi</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
288 <option value="orhinotracheale">Ornithobacterium rhinotracheale</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
289 <option value="plarvae">Paenibacillus larvae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
290 <option value="pmultocida1">Pasteurella multocida#1</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
291 <option value="pmultocida2">Pasteurella multocida#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
292 <option value="ppentosaceus">Pediococcus pentosaceus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
293 <option value="pdamselae">Photobacterium damselae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
294 <option value="psalmonis">Piscirickettsia salmonis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
295 <option value="pgingivalis">Porphyromonas gingivalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
296 <option value="pacnes">Propionibacterium acnes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
297 <option value="paeruginosa">Pseudomonas aeruginosa</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
298 <option value="pfluorescens">Pseudomonas fluorescens</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
299 <option value="pputida">Pseudomonas putida</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
300 <option value="rhodococcus">Rhodococcus spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
301 <option value="ranatipestifer">Riemerella anatipestifer</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
302 <option value="senterica">Salmonella enterica</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
303 <option value="sparasitica">Saprolegnia parasitica</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
304 <option value="shewanella">Shewanella spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
305 <option value="sinorhizobium">Sinorhizobium spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
306 <option value="saureus">Staphylococcus aureus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
307 <option value="schromogenes">Staphylococcus chromogenes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
308 <option value="sepidermidis">Staphylococcus epidermidis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
309 <option value="shaemolyticus">Staphylococcus haemolyticus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
310 <option value="shominis">Staphylococcus hominis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
311 <option value="slugdunensis">Staphylococcus lugdunensis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
312 <option value="spseudintermedius">Staphylococcus pseudintermedius</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
313 <option value="smaltophilia">Stenotrophomonas maltophilia</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
314 <option value="sagalactiae">Streptococcus agalactiae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
315 <option value="sbovis-equinus">Streptococcus bovis/equinus complex (SBSEC)</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
316 <option value="scanis">Streptococcus canis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
317 <option value="sdysgalactiae">Streptococcus dysgalactiae equisimilis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
318 <option value="sgallolyticus">Streptococcus gallolyticus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
319 <option value="soralis">Streptococcus oralis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
320 <option value="spneumoniae">Streptococcus pneumoniae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
321 <option value="spyogenes">Streptococcus pyogenes</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
322 <option value="ssuis">Streptococcus suis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
323 <option value="sthermophilus">Streptococcus thermophilus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
324 <option value="sthermophilus2">Streptococcus thermophilus#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
325 <option value="suberis">Streptococcus uberis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
326 <option value="szooepidemicus">Streptococcus zooepidemicus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
327 <option value="streptomyces">Streptomyces spp</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
328 <option value="taylorella">Taylorella spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
329 <option value="tenacibaculum">Tenacibaculum spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
330 <option value="tpallidum">Treponema pallidum</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
331 <option value="tvaginalis">Trichomonas vaginalis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
332 <option value="ureaplasma">Ureaplasma spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
333 <option value="vcholerae">Vibrio cholerae</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
334 <option value="vcholerae2">Vibrio cholerae#2</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
335 <option value="vparahaemolyticus">Vibrio parahaemolyticus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
336 <option value="vibrio">Vibrio spp.</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
337 <option value="vtapetis">Vibrio tapetis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
338 <option value="vvulnificus">Vibrio vulnificus</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
339 <option value="wolbachia">Wolbachia </option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
340 <option value="xfastidiosa">Xylella fastidiosa</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
341 <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
342 <option value="yruckeri">Yersinia ruckeri</option>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
343 </param>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
344 </when>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
345 </conditional>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
346 <param argument="--penalty" type="integer" min="0" value="100" label="MetaMLST penaty for under-represented alleles" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
347 <param argument="--minscore" type="integer" min="0" value="80" label="Minimum alignment score for each alignment to be considered valid" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
348 <param argument="--max_xm" type="integer" min="0" value="5" label="Maximum SNPs rate for each alignment to be considered valid" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
349 <param argument="--min_read_len" type="integer" min="0" value="50" label="Minimum BowTie2 alignment length" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
350 <param argument="--min_accuracy" type="float" min="0" max="1" value="0.9" label="Minimum threshold on Confidence score to pass the reconstruction step" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
351 <param argument="--nloci" type="integer" min="0" value="100" label="Do not discard samples where at least NLOCI are detected" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
352 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="true" label="Generate log file" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
353 <param name="write_sequences" type="boolean" truevalue="-a" falsevalue="" checked="false" label="Write known sequences" />
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
354 </inputs>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
355
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
356 <outputs>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
357 <collection name="report" type="list" label="${tool.name} on ${on_string} Report">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
358 <discover_datasets pattern="(?P&lt;designation&gt;[a-zA-Z0-9\-\_]+)_report\.txt$" format="tabular" directory="./out/merged" visible="false"/>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
359 </collection>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
360 <collection name="st" type="list" label="${tool.name} on ${on_string} ST">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
361 <discover_datasets pattern="(?P&lt;designation&gt;[a-zA-Z0-9\-\_]+)_ST\.txt$" format="tabular" directory="./out/merged" visible="false"/>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
362 </collection>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
363 <data name="log_file" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string} Log">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
364 <filter>log == True</filter>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
365 </data>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
366 <data name="sequence" format="txt" from_work_dir="sequences.txt" label="${tool.name} on ${on_string} Sequences">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
367 <filter>write_sequences == True</filter>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
368 </data>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
369 </outputs>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
370 <!-- <tests>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
371 <test>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
diff changeset
372 </test>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
thanhlv
parents:
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373 </tests> -->
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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374 <help><![CDATA[
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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375 ]]> </help>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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376 <citations>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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377 <citation type="doi">10.1093/nar/gkw837</citation>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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378 </citations>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
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379 </tool>