Mercurial > repos > iuc > abricate
comparison abricate.xml @ 5:f9bf6a8d8547 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
| author | iuc |
|---|---|
| date | Wed, 11 Sep 2019 23:57:17 -0400 |
| parents | 78c75f134c16 |
| children | 1bb2ba6d3d96 |
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| 4:78c75f134c16 | 5:f9bf6a8d8547 |
|---|---|
| 7 </macros> | 7 </macros> |
| 8 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
| 9 <expand macro="version_command" /> | 9 <expand macro="version_command" /> |
| 10 | 10 |
| 11 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
| 12 abricate '$file_input' | 12 #import re |
| 13 #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier) | |
| 14 | |
| 15 ln -sf '${file_input}' ${sample_name} && | |
| 16 | |
| 17 abricate ${sample_name} | |
| 13 $adv.no_header | 18 $adv.no_header |
| 14 #if $adv.min_dna_id | 19 #if $adv.min_dna_id |
| 15 --minid=$adv.min_dna_id | 20 --minid=$adv.min_dna_id |
| 16 #end if | 21 #end if |
| 17 --db=$adv.db | 22 --db=$adv.db |