annotate lrn_risk.xml @ 3:5a27ac020c9e draft

Uploaded
author greg
date Tue, 27 Jun 2023 14:02:05 +0000
parents f98c92618a6c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
1 <tool id="lrn_risk" name="PIMA: LRNRisk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
99e04eba4033 Uploaded
greg
parents:
diff changeset
2 <description>isolate classification</description>
99e04eba4033 Uploaded
greg
parents:
diff changeset
3 <macros>
99e04eba4033 Uploaded
greg
parents:
diff changeset
4 <import>macros.xml</import>
99e04eba4033 Uploaded
greg
parents:
diff changeset
5 </macros>
99e04eba4033 Uploaded
greg
parents:
diff changeset
6 <expand macro="requirements"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
8 #import re
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
9
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
10 #for $i in $blast_features_collection:
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
11 #set file_name = $i.file_name
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
12 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
13 #if $identifier.lower().startswith('features_amr'):
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
14 #set amr_determinants_input = $identifier
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
15 #else if $identifier.lower().startswith('features_vfdb'):
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
16 #set virulence_factors_input = $identifier
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
17 #end if
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
18 ln -s '$file_name' '$identifier' &&
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
19 #end for
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
20
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
21 python '$__tool_directory__/lrn_risk.py'
99e04eba4033 Uploaded
greg
parents:
diff changeset
22 --gtdb_file '$gtdb_file'
1
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
23 --virulence_factors_file '$virulence_factors_input'
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
24 --amr_determinants_file '$amr_determinants_input'
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
25 --blacklist_file '$blacklist_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
26 --vf_distribution_file '$vf_distribution_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
27 --amr_distribution_file '$amr_distribution_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
28 --blacklist_output_file '$blacklist_output_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
29 --vfdb_output_file '$vfdb_output_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
30 --amr_output_file '$amr_output_file'
99e04eba4033 Uploaded
greg
parents:
diff changeset
31 ]]></command>
99e04eba4033 Uploaded
greg
parents:
diff changeset
32 <inputs>
99e04eba4033 Uploaded
greg
parents:
diff changeset
33 <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
1
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
34 <param name="blast_features_collection" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection BLAST features databases"/>
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
35 <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
36 <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
37 <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
38 </inputs>
99e04eba4033 Uploaded
greg
parents:
diff changeset
39 <outputs>
99e04eba4033 Uploaded
greg
parents:
diff changeset
40 <data name="blacklist_output_file" format="tsv" label="${tool.name} on ${on_string} (blacklist)"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
41 <data name="vfdb_output_file" format="tsv" label="${tool.name} on ${on_string} (VFDB)"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
42 <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
43 </outputs>
99e04eba4033 Uploaded
greg
parents:
diff changeset
44 <tests>
99e04eba4033 Uploaded
greg
parents:
diff changeset
45 <test>
99e04eba4033 Uploaded
greg
parents:
diff changeset
46 <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
1
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
47 <param name="blast_features_collection">
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
48 <collection type="list">
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
49 <element name="FEATURES_AMR_database_2023_02_02.fasta" value="FEATURES_AMR_database_2023_02_02.tsv"/>
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
50 <element name="FEATURES_incompatibility_groups_database_2023_01_01.fasta" value="FEATURES_incompatibility_groups_database_2023_01_01.tsv"/>
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
51 <element name="FEATURES_vfdb_core_database_2023_03_30.fasta" value="FEATURES_vfdb_core_database_2023_03_30.tsv"/>
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
52 </collection>
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
53 </param>
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
54 <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
55 <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
56 <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
1
f98c92618a6c Uploaded
greg
parents: 0
diff changeset
57 <output name="blacklist_output_file" value="blacklist_output.tsv" ftype="tsv"/>
0
99e04eba4033 Uploaded
greg
parents:
diff changeset
58 <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
59 <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
60 </test>
99e04eba4033 Uploaded
greg
parents:
diff changeset
61 </tests>
99e04eba4033 Uploaded
greg
parents:
diff changeset
62 <help>
99e04eba4033 Uploaded
greg
parents:
diff changeset
63 **What it does**
99e04eba4033 Uploaded
greg
parents:
diff changeset
64
99e04eba4033 Uploaded
greg
parents:
diff changeset
65 Classifies isolates into "high risk" and "unlikely high risk" and provides information about prevalence of a given virulence
99e04eba4033 Uploaded
greg
parents:
diff changeset
66 gene among all publicly available genome of a given species and prevalence of a given antimicrobial resistance gene among all
99e04eba4033 Uploaded
greg
parents:
diff changeset
67 publicly available genomes of a given species.
99e04eba4033 Uploaded
greg
parents:
diff changeset
68 </help>
99e04eba4033 Uploaded
greg
parents:
diff changeset
69 <expand macro="citations"/>
99e04eba4033 Uploaded
greg
parents:
diff changeset
70 </tool>
99e04eba4033 Uploaded
greg
parents:
diff changeset
71