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1 <tool id="catchsequence" name="catchSequenceInfo" version="1.0.0">
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2 <description>catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">abricate</requirement>
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5 <requirement type="package" version="2.19.0">mlst</requirement>
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6 <!--<requirement type="package" version="6.6.0">emboss</requirement>
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7 <requirement type="package" version="1.3.2">pandas</requirement>-->
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8 </requirements>
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9
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10
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11 <command detect_errors="aggressive"><![CDATA[
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12
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13 #import re
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14 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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15 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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16 #set $named_input_files = ''
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17 #for $input_file in $input_files
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18 ## Add single quotes around each input file identifier
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19 #set $_input_file = "'{}'".format($input_file.element_identifier)
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20 ln -s '${input_file}' ${_input_file} &&
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21 #set $named_input_files = $named_input_files + ',' + $_input_file
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22 #end for
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23
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24
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25 perl '$__tool_directory__/catchsequence.pl' $named_input_files -perc $percent -res $res -plas $plas -vf $vf > "$output"
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26
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27
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28
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29 ]]></command>
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30 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
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31 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
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32
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33 <inputs>
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34 <param type="data" name="input_files" format="fasta,fasta.gz,fasta.bz2,gbk,gbk.gz,gbk.bz2" multiple="true" label="Genome fasta files"/>
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35
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36 <param name="percent" type="select" label="Percentage type:">
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37 <option value="ident">Identity</option>
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38 <option value="cov">Coverage</option>
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39 </param>
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40
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41 <param name="res" type="text" area="false" value="90.00" label="ResFinder %: " />
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42 <param name="plas" type="text" area="false" value="90.00" label="PlasmidFinder %: " />
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43 <param name="vf" type="text" area="false" value="80.00" label="VFDB %: " />
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44
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45 </inputs>
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46
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47 <outputs>
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48 <data format="tabular" name="output" />
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49 </outputs>
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50
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51 <help>
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52 catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences.
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53
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54 This tool uses ABRicate (https://github.com/tseemann/abricate) and MLST (https://github.com/tseemann/mlst) programs to get dedicated information from DNA sequences (such as resistance genes, plasmid genes, virulence genes, allele IDs and MLST number).
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55
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56
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57 </help>
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58
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59 <citations>
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60 <citation type="doi">10.1186/1471-2105-11-595</citation>
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61 <citation type="doi">10.1093/jac/dks261</citation>
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62 <citation type="doi">10.1128/AAC.02412-14</citation>
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63 <citation type="doi">10.1093/nar/gkv1239</citation>
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64 </citations>
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65
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66 </tool>
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