Mercurial > repos > card > rgi

comparison rgi.xml @ 0:715bc9aeef69 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
author card
date Wed, 27 Feb 2019 09:08:21 -0500
parents
children f96cbb663aa9
comparison
equal deleted inserted replaced
-1:000000000000 0:715bc9aeef69
1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" version="4.2.2">
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="4.2.2">rgi</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 #if $db_opts.db_opts_selector != "default":
11 rgi load
12 #if $db_opts.db_opts_selector == "local":
13 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
14 #else:
15 -i "$db_opts.rgi_db_hist"
16 #end if
17 --local
18 &&
19 #end if
20
21 rgi main
22 -i '$input_sequence'
23 -o out
24 -t $input_type
25 -a $alignment_tool
26 -n "\${GALAXY_SLOTS:-1}"
27 $include_loose
28 $low_quality
29 -d $data
30
31 #if $db_opts.db_opts_selector != "default":
32 --local
33 #end if
34 ]]></command>
35 <inputs>
36 <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"/>
37 <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">
38 <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>
39 <option value="protein">PROTEIN (Protein Sequence)</option>
40 </param>
41 <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)">
42 <option value="blast" selected="true">BLAST</option>
43 <option value="diamond">DIAMOND</option>
44 </param>
45 <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"/>
46 <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>
47 <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">
48 <option value="wgs">WGS</option>
49 <option value="plasmid">PLASMID</option>
50 <option value="chromosome">CHROMOSOME</option>
51 <option value="NA" selected="true">NA</option>
52 </param>
53 <conditional name="db_opts">
54 <param name="db_opts_selector" type="select" label="Select an RGI database">
55 <option value="default" selected="true">Default RGI database</option>
56 <option value="local">Locally installed RGI database</option>
57 <option value="hist">RGI database from your history</option>
58 </param>
59 <when value="default">
60 <param name="rgi_db_local" type="hidden" value="" />
61 <param name="rgi_db_hist" type="hidden" value="" />
62 </when>
63 <when value="local">
64 <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">
65 <options from_data_table="rgi_databases">
66 <validator type="no_options" message="No databases are available built-in"/>
67 </options>
68 </param>
69 <param name="rgi_db_hist" type="hidden" value="" />
70 </when>
71 <when value="hist">
72 <param name="rgi_db_local" type="hidden" value="" />
73 <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />
74 </when>
75 </conditional>
76 </inputs>
77 <outputs>
78 <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/>
79 <data name="summary" format="tabular" from_work_dir="out.txt" label="${tool.name} on ${on_string}: summary.txt"/>
80 </outputs>
81 <tests>
82 <test>
83 <param name="input_sequence" value="test1.fasta" />
84 <param name="input_type" value="contig" />
85 <param name="alignment_tool" value="blast" />
86 <param name="include_loose" value="false" />
87 <param name="low_quality" value="false" />
88 <param name="data" value="NA" />
89 <conditional name="db_opts">
90 <param name="db_opts_selector" value="default" />
91 </conditional>
92 <output name="summary">
93 <assert_contents>
94 <has_text text="AY123251" />
95 </assert_contents>
96 </output>
97 </test>
98 </tests>
99 <help>
100 <![CDATA[
101 Resistance Gene Identifier (RGI)
102 ================================
103
104 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.
105
106 Usage
107 -----
108
109 1. Select your input sequence (in FASTA format).
110 2. Select your input type (CONTIG or PROTEIN).
111 3. Select your alignment tool (DIAMOND or BLAST).
112 4. Specify if you want to include loose hits (YES or NO).
113 5. Specify if you want to remove temporary files (YES or NO).
114 6. Specify if you want to low quality predictions (YES or NO).
115 7. Select your data type (WGS, PLASMID, CHROMOSOME or NA).
116 8. Run the tool.
117
118 Output
119 ------
120
121 There are 2 different output files produced by `rgi`.
122
123 summary.txt
124 ^^^^^^^^^^^
125
126 A tabular file of all detected resistance genes, one gene per line.
127
128 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
129 | 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 |
130 +==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+
131 | 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 |
132 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
133
134 report.json
135 ^^^^^^^^^^^
136
137 A json version of summary.txt.
138
139 Help
140 ----
141
142 **usage:**
143 ``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]``
144
145 **optional arguments:**
146
147 - ``-h, --help``
148 show this help message and exit
149 - ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``
150 input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
151 - ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``
152 output folder and base filename
153 - ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``
154 specify data input type (default = contig)
155 - ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``
156 specify alignment tool (default = BLAST)
157 - ``-n THREADS, --num_threads THREADS``
158 number of threads (CPUs) to use in the BLAST search (default=8)
159 - ``--include_loose``
160 include loose hits in addition to strict and perfect hits
161 - ``--local``
162 use local database (default: uses database in executable directory)
163 - ``--clean``
164 removes temporary files
165 - ``--debug``
166 debug mode
167 - ``--low_quality``
168 use for short contigs to predict partial genes
169 - ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``
170 specify a data-type (default = NA)
171 - ``-v, --version``
172 prints software version number
173
174 Links
175 -----
176
177 RGI: https://card.mcmaster.ca/analyze/rgi
178
179 Github: https://github.com/arpcard/rgi
180
181 CARD database: https://card.mcmaster.ca
182 ]]>
183 </help>
184 <citations>
185 <citation type="doi">10.1093/nar/gkw1004</citation>
186 </citations>
187 </tool>