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comparison lrn_risk.xml @ 0:99e04eba4033 draft

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author greg
date Thu, 27 Apr 2023 19:22:36 +0000
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1 <tool id="lrn_risk" name="PIMA: LRNRisk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>isolate classification</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/lrn_risk.py'
9 --gtdb_file '$gtdb_file'
10 --virulence_factors_file '$virulence_factors_file'
11 --amr_determinants_file '$amr_determinants_file'
12 --blacklist_file '$blacklist_file'
13 --vf_distribution_file '$vf_distribution_file'
14 --amr_distribution_file '$amr_distribution_file'
15 --blacklist_output_file '$blacklist_output_file'
16 --vfdb_output_file '$vfdb_output_file'
17 --amr_output_file '$amr_output_file'
18 ]]></command>
19 <inputs>
20 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
21 <param name="virulence_factors_file" type="data" format="tabular,tsv" label="File containing virulence factors detected via BLAST"/>
22 <param name="amr_determinants_file" type="data" format="tabular,tsv" label="File containing Pima AMR determinants detected via BLAST"/>
23 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
24 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
25 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
26 </inputs>
27 <outputs>
28 <data name="blacklist_output_file" format="tsv" label="${tool.name} on ${on_string} (blacklist)"/>
29 <data name="vfdb_output_file" format="tsv" label="${tool.name} on ${on_string} (VFDB)"/>
30 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
35 <param name="virulence_factors_file" value="virulence_factors.tsv" ftype="tsv"/>
36 <param name="amr_determinants_file" value="amr_determinants.tsv" ftype="tsv"/>
37 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
38 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
39 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
40 <output name="blacklist_output_file" value="blacklist.tsv" ftype="tsv"/>
41 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
42 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
43 </test>
44 </tests>
45 <help>
46 **What it does**
47
48 Classifies isolates into "high risk" and "unlikely high risk" and provides information about prevalence of a given virulence
49 gene among all publicly available genome of a given species and prevalence of a given antimicrobial resistance gene among all
50 publicly available genomes of a given species.
51 </help>
52 <expand macro="citations"/>
53 </tool>
54