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comparison staramr_search.xml @ 8:da787fc8b740 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
author nml
date Mon, 24 Jun 2019 15:21:42 -0400
parents f1adc47e017a
children 61a3e97aa865
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7:f1adc47e017a 8:da787fc8b740
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #import re 11 #import re
12 12
13 #set $named_genomes = '' 13 #set $named_genomes = ''
14 #for $genome in $genomes 14 #for $genome in $genomes
15 #set $_named_genome = re.sub(r'(\s|\(|\))', '_', '"{}.fasta"'.format($genome.element_identifier)) 15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
16 ln -s "$genome" $_named_genome && 16 ln -s '$genome' $_named_genome &&
17 #set $named_genomes = $named_genomes + ' ' + $_named_genome 17 #set $named_genomes = $named_genomes + ' ' + $_named_genome
18 #end for 18 #end for
19 19
20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel) 20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
21 ln -s "$excel" $excel_proper_extension && 21 ln -s "$excel" $excel_proper_extension &&
351 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder 351 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
352 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git 352 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
353 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8 353 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
354 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51 354 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
355 pointfinder_gene_drug_version = 050218 355 pointfinder_gene_drug_version = 050218
356 resfinder_gene_drug_version = 050218.1 356 resfinder_gene_drug_version = 050218.1
357 357
358 results.xlsx 358 results.xlsx
359 ```````````` 359 ````````````
360 360
361 An Excel spreadsheet containing the previous 5 files as separate worksheets. 361 An Excel spreadsheet containing the previous 5 files as separate worksheets.
362 362
363 BLAST Hits 363 BLAST Hits
364 `````````` 364 ``````````
365 365
366 The dataset collection **hits** stores fasta files of the specific blast hits. 366 The dataset collection **hits** stores fasta files of the specific blast hits.
367 367
368 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada. 368 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
369 369
370 .. _staramr: https://github.com/phac-nml/staramr 370 .. _staramr: https://github.com/phac-nml/staramr
371 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db 371 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db