Mercurial > repos > estrain > amrfinderplus_db
comparison amrfinderplus_db/amrfinderplus_db.xml @ 2:d453f732f264 draft
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author | estrain |
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date | Tue, 24 May 2022 11:47:02 +0000 |
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children | b09b80e54642 |
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1:ba50f77b5db9 | 2:d453f732f264 |
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1 <tool id="amrfinderplus_db" name="amrfinderplus_db" version="@VERSION@+galaxy1"> | |
2 <description> | |
3 NCBI AMRFinderPlus - requires data_manager_amrfinderplus | |
4 </description> | |
5 <macros> | |
6 <token name="@VERSION@">3.10.23</token> | |
7 </macros> | |
8 <requirements> | |
9 <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement> | |
10 </requirements> | |
11 <version_command><![CDATA[amrfinder --version]]></version_command> | |
12 | |
13 <command detect_errors="exit_code"><![CDATA[ | |
14 amrfinder | |
15 $plus | |
16 --threads \${GALAXY_SLOTS:-1} | |
17 --database '$amrfinder_databases.fields.path' | |
18 #if $input_selection.input_source_selector == 'nuc' | |
19 -n '$input_selection.fasta_file' | |
20 #elif $input_selection.input_source_selector == 'pro' | |
21 -p '$input_selection.fasta_file' | |
22 #if $input_selection.gff.use == 'gff_yes' | |
23 -g '$input_selection.gff.gff_file' | |
24 #end if | |
25 #elif $input_selection.input_source_selector == 'both' | |
26 -n '$input_selection.nuc_file' | |
27 -p '$input_selection.pro_file' | |
28 #if $input_selection.gff.use == 'gff_yes' | |
29 -g '$input_selection.gff.gff_file' | |
30 #end if | |
31 #end if | |
32 #if str($organism) != 'None' | |
33 -O $organism | |
34 #end if | |
35 -o results.tsv | |
36 $report_common | |
37 #if $mutation_all == "true" | |
38 --mutation_all mutation_all.tsv | |
39 #end if | |
40 $gpipe | |
41 ]]> </command> | |
42 | |
43 <inputs> | |
44 <conditional name="input_selection"> | |
45 <param name="input_source_selector" type="select" label="Input data type"> | |
46 <option value="nuc">Nucleotide</option> | |
47 <option value="pro">Protein</option> | |
48 <option value="both">Nucleotide and Protein</option> | |
49 </param> | |
50 <when value="nuc"> | |
51 <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/> | |
52 </when> | |
53 <when value="pro"> | |
54 <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/> | |
55 <conditional name="gff"> | |
56 <param name="use" type="select" label="Using GFF to get genomic coordinates"> | |
57 <option value="gff_yes">Yes</option> | |
58 <option value="gff_no" selected="true">No</option> | |
59 </param> | |
60 <when value="gff_yes"> | |
61 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> | |
62 </when> | |
63 <when value="gff_no"> | |
64 </when> | |
65 </conditional> | |
66 </when> | |
67 <when value="both"> | |
68 <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/> | |
69 <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/> | |
70 <conditional name="gff"> | |
71 <param name="use" type="select" label="Using GFF to get genomic coordinates"> | |
72 <option value="gff_yes">Yes</option> | |
73 <option value="gff_no" selected="true">No</option> | |
74 </param> | |
75 <when value="gff_yes"> | |
76 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> | |
77 </when> | |
78 <when value="gff_no"> | |
79 </when> | |
80 </conditional> | |
81 </when> | |
82 </conditional> | |
83 <!-- DATABASE INPUT--> | |
84 <param name="amrfinder_databases" label="Select a database" type="select"> | |
85 <options from_data_table="amrfinderplus"> | |
86 <validator message="No database is available" type="no_options" /> | |
87 </options> | |
88 </param> | |
89 <param name="organism" type="select" optional="true" label="Get organism-specific results"> | |
90 <option value="Campylobacter">Campylobacter</option> | |
91 <option value="Escherichia">Escherichia</option> | |
92 <option value="Klebsiella">Klebsiella</option> | |
93 <option value="Salmonella">Salmonella</option> | |
94 <option value="Staphylococcus">Staphylococcus</option> | |
95 <option value="Vibrio">Vibrio</option> | |
96 </param> | |
97 <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" /> | |
98 <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" /> | |
99 <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" /> | |
100 <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" /> | |
101 <param name="mutation_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of mutations" /> | |
102 <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" /> | |
103 </inputs> | |
104 | |
105 <outputs> | |
106 <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/> | |
107 <data name="all_mutations" format="tabular" from_work_dir="mutation_all.tsv" label="${tool.name} on ${on_string}: All Mutations"> | |
108 <filter>mutation_all</filter> | |
109 </data> | |
110 </outputs> | |
111 | |
112 <tests> | |
113 </tests> | |
114 | |
115 | |
116 <help><![CDATA[ | |
117 This software and the accompanying database are designed to find acquired | |
118 antimicrobial resistance genes in bacterial protein or assembled nucleotide | |
119 sequences as well as known point mutations for several taxa. With | |
120 AMRFinderPlus we have added select members of additional classes of genes | |
121 such as virulence factors, biocide, heat, acid, and metal resistance genes. | |
122 More details: https://github.com/ncbi/amr/wiki | |
123 ]]> </help> | |
124 <citations> | |
125 <citation type="doi">10.1101/550707</citation> | |
126 </citations> | |
127 | |
128 </tool> |