Mercurial > repos > estrain > ncbi_amrfinderplus

comparison amrfinderplus.xml @ 6:5c967a2627d4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Thu, 25 Jun 2020 13:40:24 -0400
parents
children
comparison
equal deleted inserted replaced
5:b836150ca6aa 6:5c967a2627d4
1 <tool id="amrfinder" name="amrfinder-plus" version="@VERSION@+galaxy1">
2 <description>
3 identifies AMR genes using either protein annotations or nucleotide sequence.
4 </description>
5 <macros>
6 <token name="@VERSION@">3.8.4</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 $point_mut_all
38 --point_mut_all point_mutate.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="amrfinder_databases">
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="point_mut_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of reference point 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 ${on_string}: Result"/>
107 <data name="point_mutate" format="tabular" from_work_dir="point_mutate.tsv" label="${tool.name} on ${on_string}: Point mutate all">
108 <filter>point_mut_all</filter>
109 </data>
110 </outputs>
111
112 <tests>
113 <test> <!-- dna input-->
114 <param name="input_source_selector" value="nuc"/>
115 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
116 <param name="amrfinder_databases" value="2019-08-27.1" />
117 <output name="result" file="test_dna.expected" lines_diff="1"/>
118 </test>
119 <test> <!-- dna input and organism, plus gene-->
120 <param name="input_source_selector" value="nuc"/>
121 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
122 <param name="organism" value="Escherichia" />
123 <param name="plus" value="true" />
124 <param name="amrfinder_databases" value="2019-08-27.1" />
125 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
126 </test>
127 <test> <!-- AA input-->
128 <param name="input_source_selector" value="pro"/>
129 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
130 <param name="amrfinder_databases" value="2019-08-27.1" />
131 <output name="result" file="test_prot.expected" lines_diff="1"/>
132 </test>
133 <test> <!-- DNA and AA input-->
134 <param name="input_source_selector" value="both"/>
135 <param name="use" value="gff_yes"/>
136 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
137 <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
138 <param name="use" value="gff_yes"/>
139 <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
140 <param name="amrfinder_databases" value="2019-08-27.1" />
141 <output name="result" file="test_both.expected" lines_diff="1"/>
142 </test>
143 </tests>
144
145
146 <help><![CDATA[
147 This software and the accompanying database are designed to find acquired
148 antimicrobial resistance genes in bacterial protein or assembled nucleotide
149 sequences as well as known point mutations for several taxa. With
150 AMRFinderPlus we have added select members of additional classes of genes
151 such as virulence factors, biocide, heat, acid, and metal resistance genes.
152 More details: https://github.com/ncbi/amr/wiki
153 ]]> </help>
154 <citations>
155 <citation type="doi">10.1101/550707</citation>
156 </citations>
157
158 </tool>