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author galaxytrakr
date Thu, 26 Mar 2026 18:55:33 +0000
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1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" profile="23" version="6.0.5+gt_0.1">
2 <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
3 <requirements>
4 <requirement type="package" version="6.0.5">rgi</requirement>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7 #if $db_opts.db_opts_selector == "default":
8 export DB_PATH='${__tool_data_path__}/rgi_databases/_default' &&
9 export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
10 mkdir -p "\$DB_PATH" &&
11 #end if
12
13 #if $db_opts.db_opts_selector != "default":
14 rgi load
15 #if $db_opts.db_opts_selector == "local":
16 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
17 #else:
18 -i "$db_opts.rgi_db_hist"
19 #end if
20 --local
21 &&
22 #end if
23
24 rgi main
25 -i '$input_sequence'
26 -o out
27 -t $input_type
28 -a $alignment_tool
29 -n "\${GALAXY_SLOTS:-1}"
30 $include_loose
31 $low_quality
32 -d $data
33
34 #if $db_opts.db_opts_selector != "default":
35 --local
36 #end if
37 ]]></command>
38 <inputs>
39 <param argument="--input_sequence" type="data" format="fastq,fasta" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/>
40 <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">
41 <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>
42 <option value="protein">PROTEIN (Protein Sequence)</option>
43 </param>
44 <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)">
45 <option value="blast" selected="true">BLAST</option>
46 <option value="diamond">DIAMOND</option>
47 </param>
48 <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="include loose hits in addition to strict and perfect hits"/>
49 <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>
50 <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">
51 <option value="wgs">WGS</option>
52 <option value="plasmid">PLASMID</option>
53 <option value="chromosome">CHROMOSOME</option>
54 <option value="NA" selected="true">NA</option>
55 </param>
56 <conditional name="db_opts">
57 <param name="db_opts_selector" type="select" label="Select an RGI database">
58 <option value="default" selected="true">Default RGI database</option>
59 <option value="local">Locally installed RGI database</option>
60 <option value="hist">RGI database from your history</option>
61 </param>
62 <when value="default">
63 <param name="rgi_db_local" type="hidden" value="" />
64 <param name="rgi_db_hist" type="hidden" value="" />
65 </when>
66 <when value="local">
67 <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">
68 <options from_data_table="rgi_databases">
69 <validator type="no_options" message="No databases are available built-in"/>
70 </options>
71 </param>
72 <param name="rgi_db_hist" type="hidden" value="" />
73 </when>
74 <when value="hist">
75 <param name="rgi_db_local" type="hidden" value="" />
76 <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />
77 </when>
78 </conditional>
79 </inputs>
80 <outputs>
81 <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/>
82 <data name="summary" format="tabular" from_work_dir="out.txt" label="${tool.name} on ${on_string}: summary.txt"/>
83 </outputs>
84 <tests>
85 <test>
86 <param name="input_sequence" value="test1.fasta" />
87 <param name="input_type" value="contig" />
88 <param name="alignment_tool" value="blast" />
89 <param name="include_loose" value="false" />
90 <param name="low_quality" value="false" />
91 <param name="data" value="NA" />
92 <conditional name="db_opts">
93 <param name="db_opts_selector" value="default" />
94 </conditional>
95 <output name="summary">
96 <assert_contents>
97 <has_text text="AY123251" />
98 </assert_contents>
99 </output>
100 </test>
101 </tests>
102 <help>
103 <![CDATA[
104 Resistance Gene Identifier (RGI)
105 ================================
106
107 RGI is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The tool uses data from the CARD database.
108
109 Usage
110 -----
111
112 1. Select your input sequence (in FASTA format).
113 2. Select your input type (CONTIG or PROTEIN).
114 3. Select your alignment tool (DIAMOND or BLAST).
115 4. Specify if you want to include loose hits (YES or NO).
116 5. Specify if you want to remove temporary files (YES or NO).
117 6. Specify if you want to low quality predictions (YES or NO).
118 7. Select your data type (WGS, PLASMID, CHROMOSOME or NA).
119 8. Run the tool.
120
121 Output
122 ------
123
124 There are 2 different output files produced by `rgi`.
125
126 summary.txt
127 ^^^^^^^^^^^
128
129 A tabular file of all detected resistance genes, one gene per line.
130
131 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
132 | ORF_ID | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID |
133 +==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+
134 | AY123251.1_6 # 3575 # 4489 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399 | AY123251.1_6 | 3575 | 4489 | \+ | Strict | 500 | 506.908 | CARB-7 | 83.68 | 3002246 | protein homolog model | n/a | n/a | penam | antibiotic inactivation | CARB beta-lactamase | ATGC | MLLYKMCDNQNYGVTYMKFLLV | MKSLLVFALLMPSVVFASSSKFQSV | 105.56 | gnl|BL_ORD_ID|589|hsp_num:0 | 1443 |
135 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
136
137 report.json
138 ^^^^^^^^^^^
139
140 A json version of summary.txt.
141
142 Help
143 ----
144
145 **usage:**
146 ``rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]``
147
148 **optional arguments:**
149
150 - ``-h, --help``
151 show this help message and exit
152 - ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``
153 input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
154 - ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``
155 output folder and base filename
156 - ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``
157 specify data input type (default = contig)
158 - ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``
159 specify alignment tool (default = BLAST)
160 - ``-n THREADS, --num_threads THREADS``
161 number of threads (CPUs) to use in the BLAST search (default=8)
162 - ``--include_loose``
163 include loose hits in addition to strict and perfect hits
164 - ``--local``
165 use local database (default: uses database in executable directory)
166 - ``--clean``
167 removes temporary files
168 - ``--debug``
169 debug mode
170 - ``--low_quality``
171 use for short contigs to predict partial genes
172 - ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``
173 specify a data-type (default = NA)
174 - ``-v, --version``
175 prints software version number
176
177 Links
178 -----
179
180 RGI: https://card.mcmaster.ca/analyze/rgi
181
182 Github: https://github.com/arpcard/rgi
183
184 CARD database: https://card.mcmaster.ca
185 ]]>
186 </help>
187 <citations>
188 <citation type="doi">10.1093/nar/gkw1004</citation>
189 </citations>
190 </tool>