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comparison ResFinder.xml @ 0:a16d245332d6 draft default tip

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author dcouvin
date Wed, 08 Dec 2021 01:46:07 +0000
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1 <tool id="resfinder" name="ResFinder" version="4.0">
2 <description>identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.</description>
3
4 <requirements>
5 <requirement type="package" version="0.8.9">tabulate</requirement>
6 <requirement type="package" version="1.79">biopython</requirement>
7 <requirement type="package" version="1.5.6">cgecore</requirement>
8 <requirement type="package" version="3.1.24">gitpython</requirement>
9 <requirement type="package" version="2.8.2">python-dateutil</requirement>
10 <requirement type="package" version="2.34.1">git</requirement>
11 <requirement type="package" version="3.0.5">gcg</requirement>
12 </requirements>
13
14 <command detect_errors="aggressive"><![CDATA[
15 #import re
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 ## Add single quotes around each input file identifier
19 #set $_input_file = "'{}'".format($input.element_identifier)
20 ln -s '${input}' ${_input_file} &&
21
22 $__tool_directory__/resfinder/run_resfinder.py -s "$s" -l 0.6 -t 0.8 --acquired --point -ifa $_input_file -db_res $__tool_directory__/resfinder/db_resfinder/ -db_point $__tool_directory__/resfinder/db_pointfinder/ -o output
23 && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
24
25 ]]></command>
26
27
28 <inputs>
29
30 <param format="fasta" name="input" type="data" label="FASTA file : "/>
31
32 <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist">
33 <option value="campylobacter">Campylobacter spp.*</option>
34 <option value="campylobacter jejuni">Campylobacter jejuni*</option>
35 <option value="campylobacter coli">Campylobacter coli*</option>
36 <option value="escherichia coli">Escherichia coli*</option>
37 <option value="salmonella">Salmonella spp.*</option>
38 <option value="plasmodium falciparum">Plasmodium falciparum*</option>
39 <option value="neisseria gonorrhoeae">Neisseria gonorrhoeae*</option>
40 <option value="mycobacterium tuberculosis">Mycobacterium tuberculosis*</option>
41 <option value="enterococcus faecalis">Enterococcus faecalis*</option>
42 <option value="enterococcus faecium">Enterococcus faecium*</option>
43 <option value="klebsiella">Klebsiella*</option>
44 <option value="helicobacter pylori">Helicobacter pylori*</option>
45 <option value="staphylococcus aureus">Staphylococcus aureus*</option>
46 <option value="other">Other</option>
47 </param>
48
49 <param name="l" type="text" area="false" value="0.6" label="Minimum (breadth-of) coverage of ResFinder within the range 0-1:"/>
50 <param name="t" type="text" value="0.8" area="false" label="Threshold for identity of ResFinder within the range 0-1:"/>
51
52
53 </inputs>
54
55 <outputs>
56
57 <collection name="outputreport" type="list" label="${tool.name}: Report files">
58 <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" directory="./output" format="txt"/>
59 </collection>
60
61 <data format="fasta" name="resistance_genes" label="${tool.name}: resistance genes"/>
62
63 </outputs>
64
65
66 <help><![CDATA[
67 This tool allows to identify acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria (in FASTA format).
68
69 BitBucket: https://bitbucket.org/genomicepidemiology/resfinder/src/master/
70 ]]></help>
71
72 <citations>
73 <citation type="doi">10.1093/jac/dkaa345</citation>
74 </citations>
75
76 </tool>