Mercurial > repos > dazeone > kleborate
comparison kleborate.xml @ 12:2f40d5433416 draft
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| author | dazeone |
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| date | Tue, 16 Mar 2021 14:18:21 +0000 |
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| 11:34590dd5ed3e | 12:2f40d5433416 |
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| 1 <tool id="kleboratetool" name="Kleborate" version="0.1.0"> | |
| 2 <description>Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.0.4">kleborate</requirement> | |
| 5 <requirement type="package" version="0.5.1">kaptive</requirement> | |
| 6 <requirement type="package" version="2.10.1">blast</requirement> | |
| 7 </requirements> | |
| 8 | |
| 9 <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command> | |
| 10 | |
| 11 <inputs> | |
| 12 <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> | |
| 13 | |
| 14 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):"> | |
| 15 <option value="">no</option> | |
| 16 <option value="-r">yes</option> | |
| 17 </param> | |
| 18 | |
| 19 <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):"> | |
| 20 <option value="">no</option> | |
| 21 <option value="--kaptive_k">yes</option> | |
| 22 </param> | |
| 23 | |
| 24 <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):"> | |
| 25 <option value="">no</option> | |
| 26 <option value="--kaptive_o">yes</option> | |
| 27 </param> | |
| 28 | |
| 29 </inputs> | |
| 30 | |
| 31 <outputs> | |
| 32 <data format="tabular" name="output" /> | |
| 33 </outputs> | |
| 34 | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="input" value="KP011_S63.scfd.fasta " /> | |
| 38 <param name="input" value="KP012_S64.scfd.fasta " /> | |
| 39 <param name="r" value="-r"/> | |
| 40 <param name="kaptive_k" value="--kaptive_k"/> | |
| 41 <param name="kaptive_o" value=""/> | |
| 42 <output name="output" file="Kleborate_results.txt" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 | |
| 46 <help> | |
| 47 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki) | |
| 48 </help> | |
| 49 <citations> | |
| 50 <citation type="doi">10.1101/2020.12.14.422303</citation> | |
| 51 </citations> | |
| 52 </tool> | |
| 53 | |
| 54 | |
| 55 |