staramr: staramr_search.xml annotate

annotate staramr_search.xml @ 14:4b9a8031ab74 draft

"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit bb824050809fecf04d8f17cd4419033c18927f45"

author	nml
date	Fri, 05 Mar 2021 16:04:58 +0000
parents	2fd4d4c9c5c2
children	be818ae858e4

rev	line source
14 4b9a8031ab74 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit bb824050809fecf04d8f17cd4419033c18927f45" nml parents: 13 diff changeset	1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0">
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>
14 4b9a8031ab74 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit bb824050809fecf04d8f17cd4419033c18927f45" nml parents: 13 diff changeset	4 <token name="@VERSION@">0.7.2</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
12 aeaa20b96ef2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 014bea9d3a8d8bda2eebe4dde697b72c776ff158" nml parents: 11 diff changeset	20 #set $excel_proper_extension = '"results.xlsx"'
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	21 ln -s "$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 $advanced.plength_pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	37
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	38 #if str($advanced.mlst_scheme) != 'auto':
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	39 --mlst-scheme '${advanced.mlst_scheme}'
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	40 #end if
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	41
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	42 $advanced.report_all_blast
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	43 $advanced.exclude_negatives
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	44 $advanced.exclude_resistance_phenotypes
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	45
4 1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	46 #if str($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	47 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	48 #elif str($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	49 --no-exclude-genes
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	50 #end if
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	51
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	52 #if str($advanced.plasmidfinder_type) != 'include_all'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	53 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	54 #end if
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	55
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	56 --output-summary $summary
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	57 --output-detailed-summary $detailed_summary
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	58 --output-resfinder $resfinder
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	59 --output-plasmidfinder $plasmidfinder
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	60 #if str($use_pointfinder) != 'disabled'
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	61 --output-pointfinder $pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	62 #end if
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	63 --output-settings $settings
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	64 --output-excel $excel_proper_extension
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	65 --output-mlst $mlst
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	66
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	67 --output-hits-dir staramr_hits
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	68
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	69 #if str($use_pointfinder) != 'disabled'
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	70 --pointfinder-organism '${use_pointfinder}'
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	71 #end if
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	72
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	73 $named_genomes
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	74 ]]></command>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	75 <inputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	76 <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	77 <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	78 <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	79 <option value="salmonella">Salmonella</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	80 <option value="campylobacter">Campylobacter</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	81 </param>
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	82 <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	83 <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	84 min="0" max="100" help="(--pid-threshold)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	85 <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	86 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	87 <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	88 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	89 <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	90 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	91 <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	92 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	93 <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	94 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	95 <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	96 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	97 <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	98 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	99 <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	100 help="(--unacceptable-number-contigs)" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	101 <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	102 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	103 <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	104 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	105 <param name="mlst_scheme" type="select" label="MLST Scheme">
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	106 <option value="auto" selected="true">Automatic</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	107 <option value="abaumannii">Acinetobacter baumannii</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	108 <option value="abaumannii_2">Acinetobacter baumannii</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	109 <option value="achromobacter">Achromobacter </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	110 <option value="aeromonas">Aeromonas </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	111 <option value="afumigatus">Aspergillus afumigatus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	112 <option value="aphagocytophilum">Anaplasma aphagocytophilum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	113 <option value="arcobacter">Arcobacter </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	114 <option value="bburgdorferi">Borrelia burgdorferi</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	115 <option value="bcc">Burkholderia cepacia</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	116 <option value="bcereus">Bacillus cereus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	117 <option value="bhampsonii">Brachyspira hampsonii</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	118 <option value="bhenselae">Bartonella henselae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	119 <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	120 <option value="bifidobacterium">Bifidobacterium bifidobacterium</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	121 <option value="bintermedia">Brachyspira intermedia</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	122 <option value="blicheniformis">Bacillus licheniformis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	123 <option value="bordetella">Bordetella pertussis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	124 <option value="borrelia">Borrelia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	125 <option value="bpilosicoli">Brachyspira pilosicoli</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	126 <option value="bpseudomallei">Burkholderia pseudomallei</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	127 <option value="brachyspira">Brachyspira </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	128 <option value="bsubtilis">Bacillus subtilis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	129 <option value="calbicans">Candida albicans</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	130 <option value="campylobacter">Campylobacter coli</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	131 <option value="campylobacter">Campylobacter jejuni</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	132 <option value="cbotulinum">Clostridium botulinum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	133 <option value="cconcisus">Campylobacter concisus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	134 <option value="cdifficile">Clostridium difficile</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	135 <option value="cdifficile">Peptoclostridium difficile</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	136 <option value="cdifficile_2">Clostridium difficile</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	137 <option value="cdiphtheriae">Corynebacterium diphtheriae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	138 <option value="cfetus">Campylobacter fetus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	139 <option value="cfreundii">Citrobacter freundii</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	140 <option value="cglabrata">Candida glabrata</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	141 <option value="chelveticus">Campylobacter helveticus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	142 <option value="chlamydiales">Chlamydia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	143 <option value="chyointestinalis">Campylobacter hyointestinalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	144 <option value="cinsulaenigrae">Campylobacter insulaenigrae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	145 <option value="ckrusei">Candida krusei</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	146 <option value="clanienae">Campylobacter lanienae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	147 <option value="clari">Campylobacter lari</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	148 <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	149 <option value="cneoformans">Cryptococcus neoformans</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	150 <option value="cronobacter">Cronobacter </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	151 <option value="csepticum">Clostridium septicum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	152 <option value="csinensis">Clonorchis sinensis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	153 <option value="csputorum">Campylobacter sputorum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	154 <option value="ctropicalis">Candida tropicalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	155 <option value="cupsaliensis">Campylobacter upsaliensis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	156 <option value="ecloacae">Enterobacter cloacae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	157 <option value="ecoli">Escherichia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	158 <option value="ecoli">Shigella </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	159 <option value="ecoli_2">Escherichia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	160 <option value="edwardsiella">Edwardsiella tarda</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	161 <option value="efaecalis">Enterococcus faecalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	162 <option value="efaecium">Enterococcus faecium</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	163 <option value="fpsychrophilum">Flavobacterium psychrophilum</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	164 <option value="haemophilus">Haemophilus </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	165 <option value="hcinaedi">Helicobacter cinaedi</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	166 <option value="hinfluenzae">Haemophilus influenzae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	167 <option value="hparasuis">Haemophilus parasuis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	168 <option value="hpylori">Helicobacter pylori</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	169 <option value="hsuis">Haematopinus suis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	170 <option value="kkingae">Kingella kingae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	171 <option value="koxytoca">Klebsiella oxytoca</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	172 <option value="kpneumoniae">Klebsiella pneumoniae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	173 <option value="kseptempunctata">Kudoa septempunctata</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	174 <option value="lcasei">Lactobacillus casei</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	175 <option value="legionella">Legionella </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	176 <option value="leptospira">Leptospira </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	177 <option value="leptospira_2">Leptospira </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	178 <option value="leptospira_3">Leptospira </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	179 <option value="lmonocytogenes">Listeria monocytogenes</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	180 <option value="lsalivarius">Lactobacillus salivarius</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	181 <option value="mabscessus">Mycobacterium abscessus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	182 <option value="magalactiae">Mycoplasma agalactiae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	183 <option value="mbovis">Mycoplasma bovis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	184 <option value="mcatarrhalis">Moraxells catarrhalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	185 <option value="mhaemolytica">Mannheimia haemolytica</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	186 <option value="mhyorhinis">Mycoplasma hyorhinis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	187 <option value="mmassiliense">Mycobacterium massiliense</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	188 <option value="mplutonius">Melissococcus plutonius</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	189 <option value="neisseria">Neisseria </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	190 <option value="orhinotracheale">Ornithobacterium rhinotracheale</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	191 <option value="otsutsugamushi">Orientia tsutsugamushi</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	192 <option value="pacnes">Propionibacterium acnes</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	193 <option value="paeruginosa">Pseudomonas aeruginosa</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	194 <option value="pagglomerans">Pantoea agglomerans</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	195 <option value="pfluorescens">Pseudomonas fluorescens</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	196 <option value="pfreudenreichii">Propionibacterium freudenreichii</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	197 <option value="pgingivalis">Porphyromonas gingivalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	198 <option value="plarvae">Paenibacillus larvae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	199 <option value="pmultocida_multihost">Pasteurella multocida</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	200 <option value="pmultocida_rirdc">Pasteurella multocida</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	201 <option value="ppentosaceus">Pediococcus pentosaceus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	202 <option value="pshigelloides">Plesiomonas shigelloides</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	203 <option value="ranatipestifer">Riemerella anatipestifer</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	204 <option value="sagalactiae">Streptococcus agalactiae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	205 <option value="saureus">Staphylococcus aureus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	206 <option value="scanis">Streptococcus canis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	207 <option value="sdysgalactiae">Streptococcus dysgalactiae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	208 <option value="senterica">Salmonella enterica</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	209 <option value="sepidermidis">Staphylococcus epidermidis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	210 <option value="sgallolyticus">Streptococcus gallolyticus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	211 <option value="shaemolyticus">Staphylococcus haemolyticus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	212 <option value="shominis">Stapylococcus hominis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	213 <option value="sinorhizobium">Sinorhizobium </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	214 <option value="slugdunensis">Staphylococcus lugdunensis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	215 <option value="smaltophilia">Stenotrophomonas maltophilia</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	216 <option value="soralis">Streptococcus oralis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	217 <option value="spneumoniae">Streptococcus pneumoniae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	218 <option value="spseudintermedius">Staphylococcus pseudintermedius</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	219 <option value="spyogenes">Streptococcus pyogenes</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	220 <option value="ssuis">Streptococcus suis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	221 <option value="sthermophilus">Streptococcus thermophilus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	222 <option value="sthermophilus_2">Streptococcus thermophilus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	223 <option value="streptomyces">Streptomyces </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	224 <option value="suberis">Streptococcus uberis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	225 <option value="szooepidemicus">Streptococcus equi</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	226 <option value="taylorella">Taylorella </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	227 <option value="tenacibaculum">Tenacibaculum </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	228 <option value="tvaginalis">Trichomonas vaginalis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	229 <option value="vcholerae">Vibrio cholerae</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	230 <option value="vibrio">Vibrio </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	231 <option value="vparahaemolyticus">Vibrio parahaemolyticus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	232 <option value="vtapetis">Vibrio tapetis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	233 <option value="vvulnificus">Vibrio vulnificus</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	234 <option value="wolbachia">Wolbachia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	235 <option value="xfastidiosa">Xylella fastidiosa</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	236 <option value="yersinia">Yersinia </option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	237 <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	238 <option value="yruckeri">Yersinia ruckeri</option>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	239 </param>
4 1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	240 <conditional name="exclude_genes">
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	241 <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	242 <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	243 <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	244 <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	245 </param>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	246 <when value="default" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	247 <when value="custom">
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	248 <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	249 </when>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	250 <when value="none" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	251 </conditional>
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	252 <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	253 <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	254 <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	255 <option value="enterobacteriaceae">Enterobacteriaceae</option>
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	256 </param>
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	257 </section>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	258 </inputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	259 <outputs>
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	260 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	261 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	262 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	263 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	264 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	265 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	266 <filter>use_pointfinder != "disabled"</filter>
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	267 </data>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	268 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	269 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	270 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	271 <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	272 </collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	273 </outputs>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	274 <tests>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	275 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	276 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	277 <param name="use_pointfinder" value="salmonella" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	278
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	279 <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	280 <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	281 <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	282 <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	283 <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	284 <output_collection name="blast_hits" type="list">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	285 <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	286 <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	287 </output_collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	288 </test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	289 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	290 <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	291
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	292 <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	293 <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	294 <output_collection name="blast_hits" type="list">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	295 <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	296 </output_collection>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	297 </test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	298 <test>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	299 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	300 <section name="advanced">
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	301 <param name="mlst_scheme" value="kpneumoniae" />
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	302 </section>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	303 <output name="mlst" file="mlst.tsv" ftype="tabular" />
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	304 </test>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	305 <test>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	306 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	307 <param name="pid_threshold" value="99.8" />
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 <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	310 </test>
1 3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8 nml parents: 0 diff changeset	311 <test>
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8 nml parents: 0 diff changeset	312 <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	313 <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	314
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8 nml parents: 0 diff changeset	315 <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	316 </test>
4 1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	317 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	318 <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	319
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	320 <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	321 </test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	322 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	323 <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	324 <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	325
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	326 <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	327 </test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	328 <test>
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	329 <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	330 <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	331 <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	332
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	333 <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	334 </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	335 <test>
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5" nml parents: 9 diff changeset	336 <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	337 <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	338 <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	339
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5" nml parents: 9 diff changeset	340 <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	341 </test>
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	342 </tests>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	343 <help><![CDATA[
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	344 staramr
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	345 =======
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	346
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	347 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	348
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	349 Usage
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	350 -----
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	351
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	352 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	353 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	354 3. Run the tool.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	355
4 1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	356 Input
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	357 -----
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	358
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	359 Genomes
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	360 ```````
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	361
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	362 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	363
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	364 Exclude genes file
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	365 ``````````````````
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	366
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	367 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	368
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	369 ::
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	370
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	371 #gene_id
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	372 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	373 ColpVC_1__JX133088
4 1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446 nml parents: 3 diff changeset	374
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	375 Output
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	376 ------
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	377
9 61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	378 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	379
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	380 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	381 ````````````````````
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	382
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	383 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	384
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	385 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	386 \| 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	387 +============+==============+===================================+============+============+============+============+============+============+============+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	388 \| 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	389 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	390 \| 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	391 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71" nml parents: 8 diff changeset	392
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 summary.tsv
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
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	397 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	398
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	399 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11 5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c" nml parents: 10 diff changeset	400 \| 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 \|
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	401 +============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+
11 5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c" nml parents: 10 diff changeset	402 \| 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 \| \|
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	403 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11 5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c" nml parents: 10 diff changeset	404 \| 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 \| \|
13 2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" nml parents: 12 diff changeset	405 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11 5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c" nml parents: 10 diff changeset	406
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	407
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	408 detailed_summary.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	409 ````````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	410
7 f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	411 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	412
7 f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	413 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	414 \| 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	415 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	416 \| 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	417 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	418 \| 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	419 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	420 \| 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	421 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	422 \| 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	423 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	424 \| 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	425 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	426 \| 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	427 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	428 \| 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	429 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	430 \| 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	431 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	432 \| 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	433 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	434 \| 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	435 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	436 \| 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	437 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	438 \| 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	439 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	440 \| 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	441 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	442 \| 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	443 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	444 \| 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	445 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	446 \| 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	447 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	448 \| 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	449 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	450 \| 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	451 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	452
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	453
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	454 resfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	455 `````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	456
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	457 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	458
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	459 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	460 \| 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	461 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	462 \| 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	463 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	464 \| 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	465 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	466 \| 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	467 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	468 \| 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	469 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	470 \| 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	471 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	472 \| 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	473 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	474 \| 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	475 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	476 \| 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	477 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	478
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	479 plasmidfinder.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	480 `````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	481
7 f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	482 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	483
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	484 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
7 f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 nml parents: 6 diff changeset	485 \| 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	486 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	487 \| 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	488 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	489 \| 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	490 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	491 \| 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	492 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	493 \| 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	494 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	495 \| 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	496 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	497 \| 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	498 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	499 \| 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	500 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	501 \| 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	502 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	503
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	504 pointfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	505 ```````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	506
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	507 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	508
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	509 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	510 \| 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	511 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	512 \| 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	513 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	514 \| 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	515 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	516
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	517 settings.txt
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	518 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	519
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	520 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	521
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	522 ::
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	523
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	524 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	525 version = 0.7.1
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	526 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	527 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	528 total_minutes = 0.04
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	529 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	530 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	531 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	532 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	533 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	534 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	535 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	536 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	537 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	538 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	539 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	540 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	541 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	542 resfinder_gene_drug_version = 050218.1
0 fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	543
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	544 results.xlsx
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	545 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	546
6 3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2 nml parents: 5 diff changeset	547 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	548
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	549 BLAST Hits
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	550 ``````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	551
8 da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5 nml parents: 7 diff changeset	552 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	553
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	554 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	555
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	556 .. _staramr: https://github.com/phac-nml/staramr
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	557 .. _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	558 .. _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	559 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	560 .. _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	561 ]]></help>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	562 <citations>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	563 <citation type="bibtex">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	564 @misc{githubstaramr,
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	565 author = {Petkau, Aaron},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	566 year = {2018},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	567 title = {staramr},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	568 publisher = {GitHub},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	569 journal = {GitHub repository},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	570 url = {https://github.com/phac-nml/staramr},
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	571 }</citation>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	572 </citations>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64 nml parents: diff changeset	573 </tool>

Mercurial > repos > nml > staramr

annotate staramr_search.xml @ 14:4b9a8031ab74 draft