Mercurial > repos > dazeone > kleborate
comparison kleborate.xml @ 20:433e59fed9f8 draft
Uploaded
| author | dazeone |
|---|---|
| date | Tue, 16 Mar 2021 15:42:30 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 19:52bf903c80f2 | 20:433e59fed9f8 |
|---|---|
| 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 </requirements> | |
| 6 | |
| 7 <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command> | |
| 8 | |
| 9 <inputs> | |
| 10 <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> | |
| 11 | |
| 12 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):"> | |
| 13 <option value="">no</option> | |
| 14 <option value="-r">yes</option> | |
| 15 </param> | |
| 16 | |
| 17 <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):"> | |
| 18 <option value="">no</option> | |
| 19 <option value="--kaptive_k">yes</option> | |
| 20 </param> | |
| 21 | |
| 22 <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):"> | |
| 23 <option value="">no</option> | |
| 24 <option value="--kaptive_o">yes</option> | |
| 25 </param> | |
| 26 | |
| 27 </inputs> | |
| 28 | |
| 29 <outputs> | |
| 30 <data format="tabular" name="output" /> | |
| 31 </outputs> | |
| 32 | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="input" value="KP011_S63.scfd.fasta " /> | |
| 36 <param name="input" value="KP012_S64.scfd.fasta " /> | |
| 37 <param name="r" value="-r"/> | |
| 38 <param name="kaptive_k" value="--kaptive_k"/> | |
| 39 <param name="kaptive_o" value=""/> | |
| 40 <output name="output" file="Kleborate_results.txt" /> | |
| 41 </test> | |
| 42 </tests> | |
| 43 | |
| 44 <help> | |
| 45 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki) | |
| 46 </help> | |
| 47 <citations> | |
| 48 <citation type="doi">10.1101/2020.12.14.422303</citation> | |
| 49 </citations> | |
| 50 </tool> | |
| 51 | |
| 52 | |
| 53 |