Mercurial > repos > dazeone > kleborate
changeset 9:08985cbb9c71 draft
Deleted selected files
| author | dazeone |
|---|---|
| date | Tue, 16 Mar 2021 13:59:12 +0000 |
| parents | c78f199f5455 |
| children | f6e9040555ed |
| files | kleborate.xml |
| diffstat | 1 files changed, 0 insertions(+), 55 deletions(-) [+] |
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--- a/kleborate.xml Tue Mar 16 13:39:49 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -<tool id="kleboratetool" name="Kleborate" version="0.1.0"> - <description>Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae</description> - <requirements> - <requirement type="package" version="2.0.3">kleborate</requirement> - <requirement type="package" version="0.5.1">kaptive</requirement> - <requirement type="package" version="2.10.1">blast</requirement> -</requirements> - - <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command> - - <inputs> - <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> - - <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):"> - <option value="">no</option> - <option value="-r">yes</option> - </param> - - <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):"> - <option value="">no</option> - <option value="--kaptive_k">yes</option> - </param> - - <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):"> - <option value="">no</option> - <option value="--kaptive_o">yes</option> - </param> - - </inputs> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <tests> - <test> - <param name="input" value="KP011_S63.scfd.fasta " /> - <param name="input" value="KP012_S64.scfd.fasta " /> - <param name="r" value="-r"/> - <param name="kaptive_k" value="--kaptive_k"/> - <param name="kaptive_o" value=""/> - <output name="output" file="Kleborate_results.txt" /> - </test> -</tests> - - <help> -For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki) - </help> - <citations> - <citation type="doi">10.1101/2020.12.14.422303</citation> - </citations> -</tool> - - -