Mercurial > repos > greg > lrn_risk

comparison lrn_risk.xml @ 1:f98c92618a6c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 28 Apr 2023 15:06:29 +0000
parents 99e04eba4033
children
comparison
equal deleted inserted replaced
0:99e04eba4033 1:f98c92618a6c
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9
10 #for $i in $blast_features_collection:
11 #set file_name = $i.file_name
12 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
13 #if $identifier.lower().startswith('features_amr'):
14 #set amr_determinants_input = $identifier
15 #else if $identifier.lower().startswith('features_vfdb'):
16 #set virulence_factors_input = $identifier
17 #end if
18 ln -s '$file_name' '$identifier' &&
19 #end for
20
8 python '$__tool_directory__/lrn_risk.py' 21 python '$__tool_directory__/lrn_risk.py'
9 --gtdb_file '$gtdb_file' 22 --gtdb_file '$gtdb_file'
10 --virulence_factors_file '$virulence_factors_file' 23 --virulence_factors_file '$virulence_factors_input'
11 --amr_determinants_file '$amr_determinants_file' 24 --amr_determinants_file '$amr_determinants_input'
12 --blacklist_file '$blacklist_file' 25 --blacklist_file '$blacklist_file'
13 --vf_distribution_file '$vf_distribution_file' 26 --vf_distribution_file '$vf_distribution_file'
14 --amr_distribution_file '$amr_distribution_file' 27 --amr_distribution_file '$amr_distribution_file'
15 --blacklist_output_file '$blacklist_output_file' 28 --blacklist_output_file '$blacklist_output_file'
16 --vfdb_output_file '$vfdb_output_file' 29 --vfdb_output_file '$vfdb_output_file'
17 --amr_output_file '$amr_output_file' 30 --amr_output_file '$amr_output_file'
18 ]]></command> 31 ]]></command>
19 <inputs> 32 <inputs>
20 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/> 33 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
21 <param name="virulence_factors_file" type="data" format="tabular,tsv" label="File containing virulence factors detected via BLAST"/> 34 <param name="blast_features_collection" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection BLAST features databases"/>
22 <param name="amr_determinants_file" type="data" format="tabular,tsv" label="File containing Pima AMR determinants detected via BLAST"/>
23 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/> 35 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
24 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/> 36 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
25 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/> 37 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
26 </inputs> 38 </inputs>
27 <outputs> 39 <outputs>
30 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/> 42 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
31 </outputs> 43 </outputs>
32 <tests> 44 <tests>
33 <test> 45 <test>
34 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/> 46 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
35 <param name="virulence_factors_file" value="virulence_factors.tsv" ftype="tsv"/> 47 <param name="blast_features_collection">
36 <param name="amr_determinants_file" value="amr_determinants.tsv" ftype="tsv"/> 48 <collection type="list">
49 <element name="FEATURES_AMR_database_2023_02_02.fasta" value="FEATURES_AMR_database_2023_02_02.tsv"/>
50 <element name="FEATURES_incompatibility_groups_database_2023_01_01.fasta" value="FEATURES_incompatibility_groups_database_2023_01_01.tsv"/>
51 <element name="FEATURES_vfdb_core_database_2023_03_30.fasta" value="FEATURES_vfdb_core_database_2023_03_30.tsv"/>
52 </collection>
53 </param>
37 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/> 54 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
38 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/> 55 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
39 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/> 56 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
40 <output name="blacklist_output_file" value="blacklist.tsv" ftype="tsv"/> 57 <output name="blacklist_output_file" value="blacklist_output.tsv" ftype="tsv"/>
41 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/> 58 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
42 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/> 59 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
43 </test> 60 </test>
44 </tests> 61 </tests>
45 <help> 62 <help>