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comparison kleborate.xml @ 38:83ec88b8c1b3 draft default tip

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author dazeone
date Tue, 05 Apr 2022 15:03:17 +0000
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37:89436e9c311d 38:83ec88b8c1b3
1 <tool id="kleboratetool" name="Kleborate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description> a tool to screen genome assemblies of Klebsiella pneumoniae</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="2.1.0">kleborate</requirement>
9 <requirement type="package" version="2.0.0">kaptive</requirement>
10 </requirements>
11
12 <!-- kleborateold -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output
13 /home/linuxipg/Kleborate/kleborate-runner.py -->
14
15 <!-- <command detect_errors="aggressive"><![CDATA[
16 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
17 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
18 #set $named_input_files = ''
19 #for $input_file in $input_files
20 ## Add single quotes around each input file identifier
21 #set $_input_file = "'{}'".format($input_file.element_identifier)
22 ln -s '${input_file}' ${_input_file} &&
23 #set $named_input_files = $named_input_files + ' ' + $_input_file
24 #end for
25
26 kleborate $r $kaptive_k $kaptive_o -o $output --min_identity $ident --min_coverage $cov -a $named_input_files
27 ]]></command> -->
28
29 <inputs>
30 <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
31
32 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
33 <option value="">no</option>
34 <option value="-r">yes</option>
35 </param>
36
37 <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):">
38 <option value="">no</option>
39 <option value="--kaptive_k">yes</option>
40 </param>
41
42 <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):">
43 <option value="">no</option>
44 <option value="--kaptive_o">yes</option>
45 </param>
46
47 <param name="ident" type="text" area="false" value="90.0" label="Minimum alignment percent identity for main results:"/>
48 <param name="cov" type="text" area="false" value="80.0" label="Minimum alignment percent coverage for main results:"/>
49
50 </inputs>
51
52 <outputs>
53 <data format="tabular" name="output" />
54 </outputs>
55
56 <tests>
57 <test>
58 <param name="input" value="KP011_S63.scfd.fasta " />
59 <param name="input" value="KP012_S64.scfd.fasta " />
60 <param name="r" value="-r"/>
61 <param name="kaptive_k" value="--kaptive_k"/>
62 <param name="kaptive_o" value=""/>
63 <output name="output" file="Kleborate_results.txt" />
64 </test>
65 </tests>
66
67 <help>
68 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
69 </help>
70 <citations>
71 <citation type="doi">10.1101/2020.12.14.422303</citation>
72 <citation type="doi">10.1038/s41467-021-24448-3</citation>
73 <citation type="doi">10.1099/mgen.0.000102</citation>
74
75 </citations>
76 </tool>