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