metamlst: metamlst.xml annotate

annotate metamlst.xml @ 1:4d3e54bace61 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty"

author	thanhlv
date	Wed, 23 Feb 2022 22:57:02 +0000
parents	d1df295495a9
children

rev	line source
0 d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	3 <macros>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	5 </macros>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	6 <requirements>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	8 </requirements>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	11 #import re
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	13 #set compressed="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	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" thanhlv parents: diff changeset	15 #if str($library.type) == 'paired':
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	16 #set name_1 = re.sub('[^\w\-\s]', '_', str($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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	20 #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	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	23 #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	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	27 #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	28 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	29 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	30 ln -f -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	31
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	34 #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	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	37 #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	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" thanhlv parents: diff changeset	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" thanhlv parents: diff changeset	40 #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	41 #set read2 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	42 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	43 ln -f -s '${library.input_2}' ${read2} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	44 #else if str($library.type) == 'paired_collection':
1 4d3e54bace61 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty" thanhlv parents: 0 diff changeset	45 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.forward.name)) + "_1"
4d3e54bace61 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty" thanhlv parents: 0 diff changeset	46 #set name_2 = re.sub('[^\w\-\s]', '_', str($library.input_1.reverse.name)) + "_2"
0 d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	47 #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" thanhlv parents: diff changeset	48 #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	49 #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	50 #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" thanhlv parents: diff changeset	51 #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	52 #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	53 #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" thanhlv parents: diff changeset	54 #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	55 #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	56 #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	57 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	58 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	59 ln -s '${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" thanhlv parents: diff changeset	60
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	61 #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" thanhlv parents: diff changeset	62 #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" thanhlv parents: diff changeset	63 #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	64 #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" thanhlv parents: diff changeset	65 #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" thanhlv parents: diff changeset	66 #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	67 #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" thanhlv parents: diff changeset	68 #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" thanhlv parents: diff changeset	69 #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	70 #set read2 = $name_2 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	71 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	72 ln -s '${library.input_1.reverse}' ${read2} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	73
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	74 #else if str($library.type) == 'paired_interleaved':
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	75 #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	76 #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	77 #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	78 #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	79 #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	80 #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	81 #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	82 #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	83 #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	84 #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	85 #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	86 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	87 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	88 ln -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	89 #else:
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	90 #set name_1 = re.sub('[^\w\-\s]', '_', str($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	91 #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	92 #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	93 #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	94 #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	95 #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	96 #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	97 #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	98 #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	99 #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	100 #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	101 #set read1 = $name_1 + '.fastq'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	102 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	103 ln -s '${library.input_1}' ${read1} &&
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	104 #end if
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	105
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	106 metamlst-index.py
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	107 -i bowtie_MmetaMLST
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	108 -d '$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	109
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	110 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	111 --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	112 -a
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 --no-unal
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
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	115 ## number of threads
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	116 -p \${GALAXY_SLOTS:-4}
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	117
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	118 ## 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	119 -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	120
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 ## 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	122 #if str( $library.type ) == "single":
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	123 -U '${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	124 #elif str( $library.type ) == "paired_interleaved":
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	125 --interleaved '${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	126 #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	127 -1 '${read1}'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	128 -2 '${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	129 #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	130 \| 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	131 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	132 #if $filter_species.filter=='yes'
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	133 #set species_list = ",".join([$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	134 --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	135 #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	136 --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	137 --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	138 --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	139 --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	140 --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	141 --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	142 $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	143 $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	144 ${read1}.bam
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	145 -o ./out
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	146 -d '$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	147 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	148 #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	149 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	150 #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	151 #if $write_sequences
1 4d3e54bace61 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty" thanhlv parents: 0 diff changeset	152 cat ./out/*.nfo > sequences.txt &&
0 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 #end if
1 4d3e54bace61 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty" thanhlv parents: 0 diff changeset	154 echo "Finished"
0 d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	155 ]]> </command>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	156
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	157 <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	158 <conditional name="library">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	159 <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" thanhlv parents: diff changeset	160 <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" thanhlv parents: diff changeset	161 <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" thanhlv parents: diff changeset	162 <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" thanhlv parents: diff changeset	163 <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" thanhlv parents: diff changeset	164 </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	165
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	166 <when value="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	167 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "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	168 </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	169 <when value="paired">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	170 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file #1" help="Must be of datatype "fastqsanger"or "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	171 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTA/Q file #2" help="Must be of datatype "fastqsanger"or "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	172 </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	173 <when value="paired_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	174 <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 "fastqsanger" or "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	175 </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	176 <when value="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	177 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --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	178 </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	179 </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	180 <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" thanhlv parents: diff changeset	181 <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" thanhlv parents: diff changeset	182 <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" thanhlv parents: diff changeset	183 </options>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	184 </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	185 <conditional name="filter_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	186 <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" thanhlv parents: diff changeset	187 <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" thanhlv parents: diff changeset	188 <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" thanhlv parents: diff changeset	189 </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	190 <when value="yes">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	191 <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" thanhlv parents: diff changeset	192 <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" thanhlv parents: diff changeset	193 <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" thanhlv parents: diff changeset	194 <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" thanhlv parents: diff changeset	195 <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" thanhlv parents: diff changeset	196 <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" thanhlv parents: diff changeset	197 <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" thanhlv parents: diff changeset	198 <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" thanhlv parents: diff changeset	199 <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" thanhlv parents: diff changeset	200 <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" thanhlv parents: diff changeset	201 <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" thanhlv parents: diff changeset	202 <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" thanhlv parents: diff changeset	203 <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" thanhlv parents: diff changeset	204 <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" thanhlv parents: diff changeset	205 <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" thanhlv parents: diff changeset	206 <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" thanhlv parents: diff changeset	207 <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" thanhlv parents: diff changeset	208 <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" thanhlv parents: diff changeset	209 <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" thanhlv parents: diff changeset	210 <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" thanhlv parents: diff changeset	211 <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" thanhlv parents: diff changeset	212 <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" thanhlv parents: diff changeset	213 <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" thanhlv parents: diff changeset	214 <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" thanhlv parents: diff changeset	215 <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" thanhlv parents: diff changeset	216 <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" thanhlv parents: diff changeset	217 <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" thanhlv parents: diff changeset	218 <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" thanhlv parents: diff changeset	219 <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" thanhlv parents: diff changeset	220 <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" thanhlv parents: diff changeset	221 <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" thanhlv parents: diff changeset	222 <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" thanhlv parents: diff changeset	223 <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" thanhlv parents: diff changeset	224 <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" thanhlv parents: diff changeset	225 <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" thanhlv parents: diff changeset	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 </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	343 </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	344 </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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 </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	354
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 <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	356 <collection name="report" type="list" label="${tool.name} on ${on_string} Report">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	357 <discover_datasets pattern="(?P<designation>[a-zA-Z0-9\-\_]+)_report\.txt$" 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	358 </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	359 <collection name="st" type="list" label="${tool.name} on ${on_string} ST">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	360 <discover_datasets pattern="(?P<designation>[a-zA-Z0-9\-\_]+)_ST\.txt$" 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	361 </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	362 <data name="log_file" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string} Log">
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	363 <filter>log == True</filter>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	364 </data>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	365 <data name="sequence" format="txt" from_work_dir="sequences.txt" label="${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	366 <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	367 </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	368 </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	369 <!-- <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	370 <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	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 </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	373 <help><![CDATA[
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	374 ]]> </help>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	375 <citations>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	376 <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" thanhlv parents: diff changeset	377 </citations>
d1df295495a9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty" thanhlv parents: diff changeset	378 </tool>

Mercurial > repos > thanhlv > metamlst

annotate metamlst.xml @ 1:4d3e54bace61 draft default tip