Mercurial > repos > dazeone > kleborate
comparison kleborate.xml @ 30:aee729560f18 draft
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| author | dazeone |
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| date | Tue, 11 Jan 2022 15:58:21 +0000 |
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| 29:67f31d0be358 | 30:aee729560f18 |
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| 1 <tool id="kleboratetool" name="Kleborate" version="0.1.0"> | |
| 2 <description> a tool to screen genome assemblies of Klebsiella pneumoniae</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.1.0">kleborate</requirement> | |
| 5 <requirement type="package" version="2.0.0">kaptive</requirement> | |
| 6 </requirements> | |
| 7 | |
| 8 <!-- kleborateold -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output | |
| 9 /home/linuxipg/Kleborate/kleborate-runner.py --> | |
| 10 <command detect_errors="aggressive"><![CDATA[ | |
| 11 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' | |
| 12 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') | |
| 13 #set $named_input_files = '' | |
| 14 #for $input_file in $input_files | |
| 15 ## Add single quotes around each input file identifier | |
| 16 #set $_input_file = "'{}'".format($input_file.element_identifier) | |
| 17 ln -s '${input_file}' ${_input_file} && | |
| 18 #set $named_input_files = $named_input_files + ' ' + $_input_file | |
| 19 #end for | |
| 20 | |
| 21 kleborate $r $kaptive_k $kaptive_o -o $output --min_identity $ident --min_coverage $cov -a $named_input_files | |
| 22 ]]></command> | |
| 23 | |
| 24 <inputs> | |
| 25 <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> | |
| 26 | |
| 27 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):"> | |
| 28 <option value="">no</option> | |
| 29 <option value="-r">yes</option> | |
| 30 </param> | |
| 31 | |
| 32 <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):"> | |
| 33 <option value="">no</option> | |
| 34 <option value="--kaptive_k">yes</option> | |
| 35 </param> | |
| 36 | |
| 37 <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):"> | |
| 38 <option value="">no</option> | |
| 39 <option value="--kaptive_o">yes</option> | |
| 40 </param> | |
| 41 | |
| 42 <param name="ident" type="text" area="false" value="90.0" label="Minimum alignment percent identity for main results:"/> | |
| 43 <param name="cov" type="text" area="false" value="80.0" label="Minimum alignment percent coverage for main results:"/> | |
| 44 | |
| 45 </inputs> | |
| 46 | |
| 47 <outputs> | |
| 48 <data format="tabular" name="output" /> | |
| 49 </outputs> | |
| 50 | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="input" value="KP011_S63.scfd.fasta " /> | |
| 54 <param name="input" value="KP012_S64.scfd.fasta " /> | |
| 55 <param name="r" value="-r"/> | |
| 56 <param name="kaptive_k" value="--kaptive_k"/> | |
| 57 <param name="kaptive_o" value=""/> | |
| 58 <output name="output" file="Kleborate_results.txt" /> | |
| 59 </test> | |
| 60 </tests> | |
| 61 | |
| 62 <help> | |
| 63 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki) | |
| 64 </help> | |
| 65 <citations> | |
| 66 <citation type="doi">10.1101/2020.12.14.422303</citation> | |
| 67 <citation type="doi">10.1038/s41467-021-24448-3</citation> | |
| 68 <citation type="doi">10.1099/mgen.0.000102</citation> | |
| 69 </citations> | |
| 70 </tool> |