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1 <tool id="lrn_risk" name="PIMA: LRNRisk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>isolate classification</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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10 #for $i in $blast_features_collection:
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11 #set file_name = $i.file_name
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12 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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13 #if $identifier.lower().startswith('features_amr'):
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14 #set amr_determinants_input = $identifier
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15 #else if $identifier.lower().startswith('features_vfdb'):
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16 #set virulence_factors_input = $identifier
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17 #end if
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18 ln -s '$file_name' '$identifier' &&
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19 #end for
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20
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21 python '$__tool_directory__/lrn_risk.py'
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22 --gtdb_file '$gtdb_file'
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23 --virulence_factors_file '$virulence_factors_input'
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24 --amr_determinants_file '$amr_determinants_input'
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25 --blacklist_file '$blacklist_file'
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26 --vf_distribution_file '$vf_distribution_file'
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27 --amr_distribution_file '$amr_distribution_file'
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28 --blacklist_output_file '$blacklist_output_file'
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29 --vfdb_output_file '$vfdb_output_file'
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30 --amr_output_file '$amr_output_file'
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31 ]]></command>
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32 <inputs>
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33 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
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34 <param name="blast_features_collection" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection BLAST features databases"/>
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35 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
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36 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
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37 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
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38 </inputs>
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39 <outputs>
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40 <data name="blacklist_output_file" format="tsv" label="${tool.name} on ${on_string} (blacklist)"/>
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41 <data name="vfdb_output_file" format="tsv" label="${tool.name} on ${on_string} (VFDB)"/>
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42 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
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47 <param name="blast_features_collection">
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48 <collection type="list">
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49 <element name="FEATURES_AMR_database_2023_02_02.fasta" value="FEATURES_AMR_database_2023_02_02.tsv"/>
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50 <element name="FEATURES_incompatibility_groups_database_2023_01_01.fasta" value="FEATURES_incompatibility_groups_database_2023_01_01.tsv"/>
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51 <element name="FEATURES_vfdb_core_database_2023_03_30.fasta" value="FEATURES_vfdb_core_database_2023_03_30.tsv"/>
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52 </collection>
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53 </param>
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54 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
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55 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
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56 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
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57 <output name="blacklist_output_file" value="blacklist_output.tsv" ftype="tsv"/>
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58 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
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59 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
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60 </test>
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61 </tests>
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62 <help>
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63 **What it does**
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64
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65 Classifies isolates into "high risk" and "unlikely high risk" and provides information about prevalence of a given virulence
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66 gene among all publicly available genome of a given species and prevalence of a given antimicrobial resistance gene among all
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67 publicly available genomes of a given species.
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68 </help>
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69 <expand macro="citations"/>
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70 </tool>
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71
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