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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 python '$__tool_directory__/lrn_risk.py'
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9 --gtdb_file '$gtdb_file'
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10 --virulence_factors_file '$virulence_factors_file'
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11 --amr_determinants_file '$amr_determinants_file'
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12 --blacklist_file '$blacklist_file'
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13 --vf_distribution_file '$vf_distribution_file'
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14 --amr_distribution_file '$amr_distribution_file'
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15 --blacklist_output_file '$blacklist_output_file'
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16 --vfdb_output_file '$vfdb_output_file'
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17 --amr_output_file '$amr_output_file'
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18 ]]></command>
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19 <inputs>
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20 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
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21 <param name="virulence_factors_file" type="data" format="tabular,tsv" label="File containing virulence factors detected via BLAST"/>
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22 <param name="amr_determinants_file" type="data" format="tabular,tsv" label="File containing Pima AMR determinants detected via BLAST"/>
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23 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
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24 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
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25 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
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26 </inputs>
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27 <outputs>
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28 <data name="blacklist_output_file" format="tsv" label="${tool.name} on ${on_string} (blacklist)"/>
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29 <data name="vfdb_output_file" format="tsv" label="${tool.name} on ${on_string} (VFDB)"/>
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30 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
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35 <param name="virulence_factors_file" value="virulence_factors.tsv" ftype="tsv"/>
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36 <param name="amr_determinants_file" value="amr_determinants.tsv" ftype="tsv"/>
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37 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
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38 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
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39 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
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40 <output name="blacklist_output_file" value="blacklist.tsv" ftype="tsv"/>
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41 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
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42 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
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43 </test>
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44 </tests>
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45 <help>
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46 **What it does**
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47
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48 Classifies isolates into "high risk" and "unlikely high risk" and provides information about prevalence of a given virulence
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49 gene among all publicly available genome of a given species and prevalence of a given antimicrobial resistance gene among all
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50 publicly available genomes of a given species.
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51 </help>
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52 <expand macro="citations"/>
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53 </tool>
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54
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