Mercurial > repos > nml > staramr

annotate staramr_search.xml @ 11:5f43703968cf 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/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
author nml
date Wed, 18 Dec 2019 16:14:07 -0500
parents 7573a6c11c4d
children aeaa20b96ef2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
1 <tool id="staramr_search" name="staramr" version="@VERSION@">
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
3 <macros>
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
4 <token name="@VERSION@">0.7.1</token>
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
5 </macros>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
6 <requirements>
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
7 <requirement type="package" version="@VERSION@">staramr</requirement>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
8 </requirements>
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
9 <version_command>staramr --version</version_command>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
1
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
11 #import re
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
12
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
13 #set $named_genomes = ''
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
14 #for $genome in $genomes
8
da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
parents: 7
diff changeset
15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
parents: 7
diff changeset
16 ln -s '$genome' $_named_genome &&
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
17 #set $named_genomes = $named_genomes + ' ' + $_named_genome
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
18 #end for
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
19
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
21 ln -s "$excel" $excel_proper_extension &&
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
22
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
23 staramr search
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
24
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
25 --nprocs "\${GALAXY_SLOTS:-1}"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
26
10
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
27 --genome-size-lower-bound $advanced.genome_size_lower_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
28 --genome-size-upper-bound $advanced.genome_size_upper_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
29 --minimum-N50-value $advanced.minimum_N50_value
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
30 --minimum-contig-length $advanced.minimum_contig_length
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
31 --unacceptable-number-contigs $advanced.unacceptable_number_contigs
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
32
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
33 --pid-threshold $advanced.pid_threshold
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
34 --percent-length-overlap-resfinder $advanced.plength_resfinder
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
35 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
36 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
37
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
38 $advanced.report_all_blast
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
39 $advanced.exclude_negatives
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
40 $advanced.exclude_resistance_phenotypes
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
41
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
42 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
43 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
44 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
45 --no-exclude-genes
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
46 #end if
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
47
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
48 #if str($advanced.plasmidfinder_type) != 'include_all'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
49 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
50 #end if
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
51
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
52 --output-summary $summary
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
53 --output-detailed-summary $detailed_summary
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
54 --output-resfinder $resfinder
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
55 --output-plasmidfinder $plasmidfinder
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
56 #if str($use_pointfinder) != 'disabled'
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
57 --output-pointfinder $pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
58 #end if
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
59 --output-settings $settings
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
60 --output-excel $excel_proper_extension
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
61
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
62 --output-hits-dir staramr_hits
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
63
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
64 #if str($use_pointfinder) != 'disabled'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
65 --pointfinder-organism '${use_pointfinder}'
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
66 #end if
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
67
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
68 $named_genomes
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
69 ]]></command>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
70 <inputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
71 <param type="data" name="genomes" format="fasta" multiple="true"/>
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
72 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
73 <option value="disabled" selected="true">Disable PointFinder</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
74 <option value="salmonella">Salmonella</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
75 <option value="campylobacter">Campylobacter</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
76 </param>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
77 <section name="advanced" title="Advanced options" expanded="false">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
78 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
79 min="0" max="100" help="(--pid-threshold)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
80 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
81 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
82 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
83 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
84 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
85 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
10
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
86 <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
87 help="(--genome-size-lower-bound)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
88 <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
89 help="(--genome-size-upper-bound)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
90 <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
91 help="(--minimum-N50-value)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
92 <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
93 help="(--minimum-contig-length)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
94 <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
95 help="(--unacceptable-number-contigs)" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
96 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
97 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
98 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
99 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
100 <conditional name="exclude_genes">
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
101 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
102 <option value="default" selected="true">Exclude default list of AMR genes</option>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
103 <option value="custom">Provide a custom list of AMR genes to exclude</option>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
104 <option value="none">Do not exclude any AMR genes</option>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
105 </param>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
106 <when value="default" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
107 <when value="custom">
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
108 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
109 </when>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
110 <when value="none" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
111 </conditional>
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
112 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
113 <option value="include_all" selected="true">Include all available database types</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
114 <option value="gram_positive">Gram Positive</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
115 <option value="enterobacteriaceae">Enterobacteriaceae</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
116 </param>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
117 </section>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
118 </inputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
119 <outputs>
9
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
120 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
121 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
122 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
123 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
124 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
125 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
126 <filter>use_pointfinder != "disabled"</filter>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
127 </data>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
128 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
129 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
130 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
131 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
132 </collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
133 </outputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
134 <tests>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
135 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
136 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
9
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
137 <param name="use_pointfinder" value="salmonella" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
138
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
139 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
140 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
141 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
142 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
143 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
144 <output_collection name="blast_hits" type="list">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
145 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
146 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
147 </output_collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
148 </test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
149 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
150 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
151
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
152 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
153 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
154 <output_collection name="blast_hits" type="list">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
155 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
156 </output_collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
157 </test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
158 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
159 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
160 <param name="pid_threshold" value="99.8" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
161
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
162 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
163 </test>
1
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
164 <test>
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
165 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
166 <param name="pid_threshold" value="99.8" />
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
167
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
168 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
parents: 0
diff changeset
169 </test>
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
170 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
171 <param name="genomes" value="test-aminoglycoside.fsa" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
172
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
173 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
174 </test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
175 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
176 <param name="genomes" value="test-aminoglycoside.fsa" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
177 <param name="exclude_genes_condition" value="none" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
178
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
179 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
180 </test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
181 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
182 <param name="genomes" value="test-aminoglycoside.fsa" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
183 <param name="exclude_genes_condition" value="custom" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
184 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
185
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
186 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
187 </test>
10
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
188 <test>
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
189 <param name="genomes" value="test-aminoglycoside.fsa" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
190 <param name="genome_size_lower_bound" value="1" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
191 <param name="genome_size_upper_bound" value="10" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
192
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
193 <output name="summary" file="test8-summary.tsv" ftype="tabular"/>
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents: 9
diff changeset
194 </test>
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
195 </tests>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
196 <help><![CDATA[
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
197 staramr
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
198 =======
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
199
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
200 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
201
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
202 Usage
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
203 -----
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
204
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
205 1. Select your genome contigs (in FASTA format).
5
930893c83a1a planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents: 4
diff changeset
206 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
207 3. Run the tool.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
208
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
209 Input
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
210 -----
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
211
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
212 Genomes
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
213 ```````
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
214
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
215 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
216
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
217 Exclude genes file
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
218 ``````````````````
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
219
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
220 Setting **Provide a custom list of AMR genes to exclude** in the **Advanced options** allows you to pass a file containing a list of genes to exclude from the results. The file must start with a line **#gene_id** and the gene names must correspond to the sequence IDs in the ResFinder/PointFinder databases. For example:
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
221
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
222 ::
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
223
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
224 #gene_id
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
225 aac(6')-Iaa_1_NC_003197
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
226 ColpVC_1__JX133088
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
227
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
228 Output
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
229 ------
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
230
9
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
231 There are 6 different output files produced by `staramr` as well as a collection of additional files.
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
232
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
233 mlst.tsv
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
234 ````````````````````
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
235
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
236 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
237
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
238 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
239 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
240 +============+==============+===================================+============+============+============+============+============+============+============+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
241 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
242 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
243 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
244 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
245
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
246
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
247 summary.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
248 ```````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
249
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
250 A summary of all detected AMR genes/mutations in each genome, one genome per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
251
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
252 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
253 |------------|----------------|-----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------|-------------------------------------|-----------|---------------|---------------|-----------|---------------------------------------------------|-------------------------|
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
254 | SRR1952908 | Passed | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4796082 | 225419 | 59 | |
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
255 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | |
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
256
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
257
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
258 detailed_summary.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
259 ````````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
260
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
261 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
262
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
263 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
264 | Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
265 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
266 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
267 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
268 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
269 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
270 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
271 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
272 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
273 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
274 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
275 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
276 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
277 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
278 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
279 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
280 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
281 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
282 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
283 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
284 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
285 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
286 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
287 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
288 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
289 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
290 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
291 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
292 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
293 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
294 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
295 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
296 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
297 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
298 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
299 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
300 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
301 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
302
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
303
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
304 resfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
305 `````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
306
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
307 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
308
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
309 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
310 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
311 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
312 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
313 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
314 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
315 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
316 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
317 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
318 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
319 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
320 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
321 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
322 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
323 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
324 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
325 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
326 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
327 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
328
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
329 plasmidfinder.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
330 `````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
331
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
332 A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line.
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
333
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
334 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
335 | Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
336 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
337 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
338 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
339 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
340 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
341 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
342 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
343 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
344 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
345 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
346 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
347 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
348 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
349 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
350 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
351 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
352 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
353
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
354 pointfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
355 ```````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
356
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
357 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
358
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
359 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
360 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
361 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
362 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
363 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
364 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
365 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
366
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
367 settings.txt
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
368 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
369
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
370 The command-line, database versions, and other settings used to run `staramr`.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
371
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
372 ::
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
373
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
374 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
375 version = 0.7.1
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
376 start_time = 2019-04-25 16:01:32
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
377 end_time = 2019-04-25 16:01:34
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
378 total_minutes = 0.04
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
379 resfinder_db_dir = staramr/databases/data/dist/resfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
380 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
381 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
382 resfinder_db_date = Mon, 16 Jul 2018 16:58
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
383 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
384 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
385 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
386 pointfinder_db_date = Wed, 04 Jul 2018 14:27
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
387 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
388 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
389 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
390 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
391 pointfinder_gene_drug_version = 050218
8
da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
parents: 7
diff changeset
392 resfinder_gene_drug_version = 050218.1
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
393
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
394 results.xlsx
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
395 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
396
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
397 An Excel spreadsheet containing the previous 5 files as separate worksheets.
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
398
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
399 BLAST Hits
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
400 ``````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
401
8
da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
parents: 7
diff changeset
402 The dataset collection **hits** stores fasta files of the specific blast hits.
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
403
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
404 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
405
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
406 .. _staramr: https://github.com/phac-nml/staramr
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
407 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
408 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
409 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
410 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
411 ]]></help>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
412 <citations>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
413 <citation type="bibtex">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
414 @misc{githubstaramr,
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
415 author = {Petkau, Aaron},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
416 year = {2018},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
417 title = {staramr},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
418 publisher = {GitHub},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
419 journal = {GitHub repository},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
420 url = {https://github.com/phac-nml/staramr},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
421 }</citation>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
422 </citations>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
423 </tool>