biohansel: biohansel.xml annotate

annotate biohansel.xml @ 2:aaab9b598c9e draft

planemo upload for repository https://github.com/phac-nml/biohansel commit ccca6fffc0f2be9776f48be3d9c4082428c84a99

author	nml
date	Wed, 07 Nov 2018 10:19:04 -0500
parents	1f8eccf9d15d
children	c1d05dd90ef2

rev	line source
2 aaab9b598c9e planemo upload for repository https://github.com/phac-nml/biohansel commit ccca6fffc0f2be9776f48be3d9c4082428c84a99 nml parents: 1 diff changeset	1 <tool id="biohansel" name="biohansel" version="2.1.1">
0 c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	2 <description>SNP subtyping of genome sequence reads or assemblies</description>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	3 <requirements>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	4 <requirement type="package" version="2.1.0">bio_hansel</requirement>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	5 </requirements>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	6 <command detect_errors="exit_code">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	7 <![CDATA[
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	8
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	9 #import re
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	10
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
1 1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+\|\d+):((forward\|reverse)(_\d+)?)\.fastq(\.gz\|sanger)?$')
0 c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	14
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	15 #def is_gzipped_fastq($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	16 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	17 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	18 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	19
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	20 #def get_fastq_ext($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	21 ## Get file extension for FASTQ data param
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	22 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	23 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	24
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	25 #def base_sample_name($name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	26 ## Get the base sample name and append 1/2 depending on if forward/reverse read
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	27 #set $illumina_match = $ILLUMINA_REGEX.match($name)
1 1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	28 #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name)
1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	29
0 c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	30 #if $illumina_match
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	31 #return $illumina_match.group(1)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	32 #elif $re.search(r'_R(1\|2)', $name):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	33 #return $re.sub(r'(.+)_R(1\|2)([^\.]*)(\..+)', r'\1\3', $name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	34 #elif $re.match(r'.+_\d\.', $name):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	35 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
1 1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	36 #elif $fastq_dump_match
1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	37 #return $fastq_dump_match.group(1)
1f8eccf9d15d planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3 nml parents: 0 diff changeset	38 #else
0 c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	39 #return $name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	40 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	41 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	42
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	43 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	44 ## Get paired FASTQ filename for a data param with appropriate file extension
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	45 ## with '_1' or '_2' appended if forward or reverse reads, respectively.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	46 #set $name = $name if $name is not None else $data_input.name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	47 #set $name = $base_sample_name($name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	48 #set $postfix = '1' if $is_forward else '2'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	49 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input))
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	50 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	51 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	52
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	53 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta\|.fastq\|.fastq.gz)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	54 #if $input.type == 'fasta'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	55 #set $input_files = '"{}"'.format($input.fasta.name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	56 ln -s "$input.fasta" $input_files &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	57 #elif $input.type == 'paired'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	58 #set $forward_filename = $get_paired_fastq_filename($input.forward)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	59 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	60 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	61 ln -s "$input.forward" $forward_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	62 ln -s "$input.reverse" $reverse_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	63 #elif $input.type == 'single'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	64 #set $input_files = '"{}"'.format($input.single.name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	65 ln -s "$input.single" $input_files &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	66 #elif $input.type == 'paired_collection'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	67 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	68 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	69 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	70 ln -s "$input.paired_collection.forward" $forward_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	71 ln -s "$input.paired_collection.reverse" $reverse_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	72 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	73
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	74 ## Checking for custom scheme.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	75 #if $type_of_scheme.scheme_type == "custom":
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	76 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	77 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	78 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	79 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	80
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	81 #def get_subtype_metadata_filename($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	82 ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	83 #set $filename = $data_input.name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	84 #if $data_input.is_of_type('tabular')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	85 #return '{}.tab'.format($filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	86 #elif $data_input.is_of_type('csv')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	87 #return '{}.csv'.format($filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	88 #else
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	89 #return None
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	90 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	91 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	92
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	93 ## Symlink to subtype metadata table if it is specified
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	94 #if $subtype_metadata
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	95 #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	96 #if $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	97 ln -s '$subtype_metadata' '$subtype_metadata_filename' &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	98 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	99 #else
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	100 #set global $subtype_metadata_filename = None
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	101 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	102
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	103 #################################
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	104 ## biohansel command starts here:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	105 #################################
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	106 hansel
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	107 -vvv
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	108 -t "\${GALAXY_SLOTS:-1}"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	109 -o results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	110 -O match_results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	111 -S tech_results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	112 $dev_args.use_json
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	113 $input_files
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	114 --scheme
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	115 #if $type_of_scheme.scheme_type == "custom":
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	116 '$type_of_scheme.scheme_input.name'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	117 #else:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	118 $type_of_scheme.scheme_type
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	119 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	120 #if $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	121 --scheme-metadata $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	122 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	123 #if $kmer_vals.kmer_min
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	124 --min-kmer-freq $kmer_vals.kmer_min
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	125 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	126 #if $kmer_vals.kmer_max
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	127 --max-kmer-freq $kmer_vals.kmer_max
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	128 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	129 #if $qc_vals.low_cov_depth_freq
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	130 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	131 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	132 #if $qc_vals.max_missing_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	133 --max-missing-tiles $qc_vals.max_missing_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	134 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	135 #if $qc_vals.min_ambiguous_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	136 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	137 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	138 #if $qc_vals.max_intermediate_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	139 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	140 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	141 #if $qc_vals.low_coverage_warning
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	142 --low-cov-warning $qc_vals.low_coverage_warning
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	143 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	144 ]]>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	145 </command>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	146 <inputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	147 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	148 <param name="type" type="select" label="Sequence Data Type">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	149 <option value="fasta">Contigs (FASTA)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	150 <option value="paired">Paired-end reads (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	151 <option value="single">Single-end reads (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	152 <option value="paired_collection">Paired-end reads collection (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	153 </param>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	154 <when value="fasta">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	155 <param name="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	156 type="data" format="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	157 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	158 label="Contigs (FASTA)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	159 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	160 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	161 <when value="paired">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	162 <param name="forward"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	163 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	164 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	165 label="Forward reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	166 help="Must have ASCII encoded quality scores"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	167 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	168 <param name="reverse"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	169 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	170 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	171 label="Reverse reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	172 help="File format must match the Forward FASTQ file"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	173 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	174 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	175 <when value="single">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	176 <param name="single"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	177 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	178 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	179 label="Single-end reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	180 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	181 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	182 <when value="paired_collection">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	183 <param name="paired_collection"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	184 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	185 collection_type="paired"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	186 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	187 label="Paired-end reads collection (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	188 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	189 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	190 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	191 <conditional name="type_of_scheme">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	192 <param name="scheme_type" type="select"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	193 label="SNP Subtyping Scheme"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	194 help="Select the SNP subtyping scheme you wish to subtype with">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	195 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	196 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	197 <option value="custom">Specify your own custom scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	198 </param>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	199 <when value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	200 <when value="enteritidis"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	201 <when value="custom">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	202 <param name="scheme_input"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	203 type="data" format="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	204 label="Your biohansel SNP Subtyping Scheme"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	205 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	206 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	207 <param name="subtype_metadata"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	208 type="data" format="tabular,csv"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	209 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	210 label="Scheme Subtype Metadata Table [Optional]"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	211 help="CSV or tab-delimited format only. Must contain a 'subtype' column."
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	212 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	213 <!-- K-mer frequencies. -->
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	214 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	215 <param name="kmer_min" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	216 argument="--min-kmer-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	217 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	218 min="0" value="8"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	219 label="Min k-mer frequency/coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	220 help="default = 8"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	221 <param name="kmer_max" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	222 argument="--max-kmer-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	223 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	224 min="1" value="1000"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	225 label="Max k-mer frequency/coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	226 help="default = 1000"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	227 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	228 <!-- Quality Checking Parameters -->
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	229 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	230 <param name="low_cov_depth_freq" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	231 argument="--low-cov-depth-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	232 value="20" min="0"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	233 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	234 label="QC: Frequency below this coverage are considered low coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	235 help="default = 20"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	236 <param name="min_ambiguous_tiles" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	237 argument="--min-ambiguous-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	238 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	239 value="3" min="0"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	240 label="QC: Min number of tiles missing for Ambiguous Result"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	241 help="default = 3"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	242 <param name="max_missing_tiles" type="float"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	243 argument="--max-missing-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	244 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	245 value="0.05" min="0" max="1"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	246 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	247 <param name="max_intermediate_tiles" type="float"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	248 argument="--max-intermediate-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	249 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	250 value="0.05" min="0" max="1"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	251 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	252 help="default = 0.05, valid values {0.0 - 1.0}"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	253 <param name="low_coverage_warning" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	254 argument="--low-cov-warning"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	255 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	256 value="20"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	257 label="QC: Overall tile coverage below this value will trigger a low coverage warning"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	258 help="default = 20"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	259 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	260 <section name="dev_args" title="Developer Options" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	261 <param name="use_json"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	262 type="boolean"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	263 checked="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	264 truevalue="--json"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	265 falsevalue=""
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	266 label="Output JSON results"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	267 help="Use this option of you need json representations of analysis' details"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	268 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	269 </inputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	270 <outputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	271 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	272 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	273 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	274 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	275 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	276 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	277 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	278 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	279 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	280 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	281 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	282 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	283 </outputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	284 <tests>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	285 <test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	286 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	287 <param name="type" value="fasta"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	288 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	289 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	290 <param name="type_of_scheme" value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	291 <output name="results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	292 value="SRR1002850_SMALL.fasta-results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	293 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	294 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	295 delta="1000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	296 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	297 <output name="match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	298 value="SRR1002850_SMALL.fasta-match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	299 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	300 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	301 delta="16000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	302 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	303 <output name="tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	304 value="SRR1002850_SMALL.fasta-tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	305 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	306 lines_diff="0">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	307 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	308 </test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	309 <test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	310 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	311 <param name="type" value="paired"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	312 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	313 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	314 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	315 <param name="type_of_scheme" value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	316 <output name="tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	317 value="SRR5646583_SMALL-tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	318 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	319 lines_diff="0">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	320 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	321 <output name="results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	322 value="SRR5646583_SMALL-results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	323 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	324 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	325 delta="1000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	326 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	327 <output name="match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	328 value="SRR5646583_SMALL-match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	329 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	330 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	331 delta="16000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	332 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	333 </test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	334 </tests>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	335 <help><![CDATA[
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	336 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	337
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	338 Usage
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	339
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	340 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	341 2) Select subtyping scheme (e.g. Salmonella enterica serovar Heidelberg subtyping scheme, Salmonella enterica serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	342 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	343 4) Click ``Execute``
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	344
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	345 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	346
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	347
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	348 Example analysis results of a single FASTA file
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	349
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	350 Contents of ``results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	351
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	352 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	353 \| sample \| scheme \| scheme_version \| subtype \| all_subtypes \| tiles_matching_subtype \| are_subtypes_consistent \| inconsistent_subtypes \| n_tiles_matching_all \| n_tiles_matching_all_expected \| n_tiles_matching_positive \| n_tiles_matching_positive_expected \| n_tiles_matching_subtype \| n_tiles_matching_subtype_expected \| file_path \| qc_status \| qc_message \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	354 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	355 \| SRR1002850_SMALL \| heidelberg \| 0.5.0 \| 2.2.2.2.1.4 \| 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 \| 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 \| True \| \| 202 \| 202 \| 17 \| 17 \| 3 \| 3 \| SRR1002850_SMALL.fasta \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	356 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	357
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	358
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	359 Contents of ``match_results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	360
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	361 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	362 \| tilename \| seq \| is_revcomp \| contig_id \| match_index \| refposition \| subtype \| is_pos_tile \| sample \| file_path \| scheme \| scheme_version \| qc_status \| qc_message \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	363 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	364 \| 2154958-2.2.2.2.1.4 \| GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG \| True \| NODE_1_length_726282_cov_40.4705_ID_1 \| 13732 \| 2154958 \| 2.2.2.2.1.4 \| True \| SRR1002850_SMALL \| SRR1002850_SMALL.fasta \| heidelberg \| 0.5.0 \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	365 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	366 \| negative2131791-2.2.3.1.3 \| GCTGGGCGAAATGATGCAGTTCACCACTTGCTC \| True \| NODE_1_length_726282_cov_40.4705_ID_1 \| 36900 \| 2131791 \| 2.2.3.1.3 \| False \| SRR1002850_SMALL \| SRR1002850_SMALL.fasta \| heidelberg \| 0.5.0 \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	367 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	368
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	369 Next 201 lines omitted.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	370
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	371
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	372
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	373 Example analysis results of a single FASTQ readset
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	374
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	375
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	376 Contents of ``results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	377
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	378 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	379 \| sample \| scheme \| scheme_version \| subtype \| all_subtypes \| tiles_matching_subtype \| are_subtypes_consistent \| inconsistent_subtypes \| n_tiles_matching_all \| n_tiles_matching_all_expected \| n_tiles_matching_positive \| n_tiles_matching_positive_expected \| n_tiles_matching_subtype \| n_tiles_matching_subtype_expected \| file_path \| avg_tile_coverage \| qc_status \| qc_message \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	380 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	381 \| SRR5646583_SMALL \| heidelberg \| 0.5.0 \| 2.2.1.1.1.1 \| 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 \| 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 \| True \| \| 202 \| 202 \| 20 \| 20 \| 2 \| 2 \| ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] \| 42.631 \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	382 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	383
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	384 Contents of ``match_results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	385
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	386 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	387 \| tilename \| seq \| freq \| refposition \| subtype \| is_pos_tile \| is_kmer_freq_okay \| sample \| scheme \| scheme_version \| qc_status \| qc_message \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	388 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	389 \| negative4642573-1.2 \| TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT \| 62 \| 4642573 \| 1.2 \| False \| True \| SRR5646583_SMALL \| heidelberg \| 0.5.0 \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	390 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	391 \| 21097-2.2.1.1.1 \| GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT \| 42 \| 21097 \| 2.2.1.1.1 \| True \| True \| SRR5646583_SMALL \| heidelberg \| 0.5.0 \| PASS \| \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	392 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	393
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	394 Next 202 lines omitted.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	395
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	396
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	397 Example Subtype Metadata
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	398
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	399 A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	400
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	401
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	402 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	403 \| subtype \| clade \| source \| disease_symptoms \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	404 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	405 \| 1 \| I \| geese \| death \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	406 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	407 \| 1.1 \| I \| moose \| burns \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	408 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	409 \| 2.2.1.1.1 \| II \| mouse \| boils \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	410 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	411 \| 2.2.2.2.1.4 \| IIa \| house \| rash \|
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	412 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	413
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	414 The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	415
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	416
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	417 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	418
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	419 ]]></help>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	420 <citations>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	421 <citation type="bibtex">@ARTICLE{a1,
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	422 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	423 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	424 url = {https://github.com/phac-nml/bio_hansel}
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	425 }
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	426 }</citation>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	427 </citations>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c nml parents: diff changeset	428 </tool>

Mercurial > repos > nml > biohansel

annotate biohansel.xml @ 2:aaab9b598c9e draft