Mercurial > repos > nml > staramr
comparison staramr_search.xml @ 1:3801ea82c888 draft
planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
| author | nml |
|---|---|
| date | Mon, 18 Jun 2018 18:08:22 -0400 |
| parents | fef5aff062c7 |
| children | 0cf6774c0da6 |
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| 0:fef5aff062c7 | 1:3801ea82c888 |
|---|---|
| 2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> | 2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.2.0">staramr</requirement> | 4 <requirement type="package" version="0.2.0">staramr</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 #import re | |
| 8 | |
| 7 #set $named_genomes = '' | 9 #set $named_genomes = '' |
| 8 #for $genome in $genomes | 10 #for $genome in $genomes |
| 9 #set $_named_genome = '"{}.fasta"'.format($genome.element_identifier) | 11 #set $_named_genome = re.sub(r'(\s|\(|\))', '_', '"{}.fasta"'.format($genome.element_identifier)) |
| 10 ln -s "$genome" $_named_genome && | 12 ln -s "$genome" $_named_genome && |
| 11 #set $named_genomes = $named_genomes + ' ' + $_named_genome | 13 #set $named_genomes = $named_genomes + ' ' + $_named_genome |
| 12 #end for | 14 #end for |
| 13 | 15 |
| 14 #set $excel_proper_extension = '"{}.xlsx"'.format($excel) | 16 #set $excel_proper_extension = '"{}.xlsx"'.format($excel) |
| 107 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 109 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> |
| 108 <param name="pid_threshold" value="99.8" /> | 110 <param name="pid_threshold" value="99.8" /> |
| 109 | 111 |
| 110 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> | 112 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> |
| 111 </test> | 113 </test> |
| 114 <test> | |
| 115 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" /> | |
| 116 <param name="pid_threshold" value="99.8" /> | |
| 117 | |
| 118 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> | |
| 119 </test> | |
| 112 </tests> | 120 </tests> |
| 113 <help><![CDATA[ | 121 <help><![CDATA[ |
| 114 staramr | 122 staramr |
| 115 ======= | 123 ======= |
| 116 | 124 |