Mercurial > repos > nml > biohansel

annotate biohansel.xml @ 4:23fbe781ce41 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/biohansel commit 369308400b3da271319e5ca89245bde68ece87de
author nml
date Wed, 28 Nov 2018 09:20:07 -0500
parents c1d05dd90ef2
children c0b8de7aa02e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
23fbe781ce41 planemo upload for repository https://github.com/phac-nml/biohansel commit 369308400b3da271319e5ca89245bde68ece87de
nml
parents: 3
diff changeset
1 <tool id="biohansel" name="biohansel" version="2.1.3">
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 = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
3
c1d05dd90ef2 planemo upload for repository https://github.com/phac-nml/biohansel commit 38c1ecfc8847bbd25f66a78bfa99c753e2cbc4d2
nml
parents: 2
diff changeset
13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger|sanger\.gz)?$')
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 $subtype_metadata_filename
4
23fbe781ce41 planemo upload for repository https://github.com/phac-nml/biohansel commit 369308400b3da271319e5ca89245bde68ece87de
nml
parents: 3
diff changeset
121 --scheme-metadata '$subtype_metadata_filename'
0
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>