comparison staramr_search.xml @ 0:fef5aff062c7 draft

planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
author nml
date Wed, 06 Jun 2018 14:20:58 -0400
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1 <tool id="staramr_search" name="staramr" version="0.2.0">
2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
3 <requirements>
4 <requirement type="package" version="0.2.0">staramr</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #set $named_genomes = ''
8 #for $genome in $genomes
9 #set $_named_genome = '"{}.fasta"'.format($genome.element_identifier)
10 ln -s "$genome" $_named_genome &&
11 #set $named_genomes = $named_genomes + ' ' + $_named_genome
12 #end for
13
14 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
15 ln -s "$excel" $excel_proper_extension &&
16
17 staramr search
18
19 --nprocs "\${GALAXY_SLOTS:-1}"
20
21 --pid-threshold $advanced.pid_threshold
22 --percent-length-overlap-resfinder $advanced.plength_resfinder
23 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
24
25 $advanced.report_all_blast
26 $advanced.exclude_negatives
27 $advanced.exclude_resistance_phenotypes
28
29 --output-summary $summary
30 --output-resfinder $resfinder
31 #if $use_pointfinder.enable
32 --output-pointfinder $pointfinder
33 #end if
34 --output-settings $settings
35 --output-excel $excel_proper_extension
36
37 --output-hits-dir staramr_hits
38
39 #if $use_pointfinder.enable
40 --pointfinder-organism $use_pointfinder.organism
41 #end if
42
43 $named_genomes
44 ]]></command>
45 <inputs>
46 <param type="data" name="genomes" format="fasta" multiple="true"/>
47 <conditional name="use_pointfinder">
48 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
49 <when value="true">
50 <param name="organism" type="select" label="Select a pointfinder organism">
51 <option value="salmonella" selected="true">Salmonella</option>
52 </param>
53 </when>
54 <when value="false" />
55 </conditional>
56 <section name="advanced" title="Advanced options" expanded="false">
57 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
58 min="0" max="100" help="(--pid-threshold)" />
59 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
60 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
61 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
62 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
63 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
64 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
65 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
66 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
67 </section>
68 </inputs>
69 <outputs>
70 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
71 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
72 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
73 <filter>use_pointfinder['enable']</filter>
74 </data>
75 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
76 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
77 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
78 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
79 </collection>
80 </outputs>
81 <tests>
82 <test>
83 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
84 <conditional name="use_pointfinder">
85 <param name="enable" value="true" />
86 <param name="organism" value="salmonella" />
87 </conditional>
88
89 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
90 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
91 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
92 <output_collection name="blast_hits" type="list">
93 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
94 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
95 </output_collection>
96 </test>
97 <test>
98 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
99
100 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
101 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
102 <output_collection name="blast_hits" type="list">
103 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
104 </output_collection>
105 </test>
106 <test>
107 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
108 <param name="pid_threshold" value="99.8" />
109
110 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
111 </test>
112 </tests>
113 <help><![CDATA[
114 staramr
115 =======
116
117 staramr_ scans bacterial genome contigs against both the ResFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
118
119 Usage
120 -----
121
122 1. Select your genome contigs (in FASTA format).
123 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
124 3. Run the tool.
125
126 Output
127 ------
128
129 There are 5 different output files produced by `staramr` as well as a collection of additional files.
130
131 summary.tsv
132 ```````````
133
134 A summary of all detected AMR genes/mutations in each genome, one genome per line.
135
136 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
137 | Isolate ID | Genotype | Predicted Phenotype |
138 +============+===========================================================+===========================================================================================================+
139 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline |
140 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
141 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline |
142 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
143
144 resfinder.tsv
145 `````````````
146
147 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
148
149 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
150 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
151 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
152 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
153 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
154 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
155 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
156 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
157 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
158 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
159 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
160 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
161 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
162 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
163 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
164 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
165 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
166 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
167 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
168
169 pointfinder.tsv
170 ```````````````
171
172 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
173
174 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
175 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
176 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
177 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
178 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
179 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
180 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
181
182 settings.txt
183 ````````````
184
185 The command-line, database versions, and other settings used to run `staramr`.
186
187 ::
188
189 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
190 version = 0.2.0
191 start_time = 2018-06-05 14:41:44
192 end_time = 2018-06-05 14:41:47
193 total_minutes = 0.05
194 resfinder_db_dir = staramr/databases/data/dist/resfinder
195 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
196 resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2
197 resfinder_db_date = Tue, 20 Mar 2018 16:49
198 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
199 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
200 pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a
201 pointfinder_db_date = Fri, 06 Apr 2018 09:02
202 pointfinder_gene_drug_version = 050218
203 resfinder_gene_drug_version = 050218
204
205 results.xlsx
206 ````````````
207
208 An Excel spreadsheet containing the previous 4 files as separate worksheets.
209
210 BLAST Hits
211 ``````````
212
213 The dataset collection **hits** stores fasta files of the specific blast hits.
214
215 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
216
217 .. _staramr: https://github.com/phac-nml/staramr
218 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
219 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
220 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
221 ]]></help>
222 <citations>
223 <citation type="bibtex">
224 @misc{githubstaramr,
225 author = {Petkau, Aaron},
226 year = {2018},
227 title = {staramr},
228 publisher = {GitHub},
229 journal = {GitHub repository},
230 url = {https://github.com/phac-nml/staramr},
231 }</citation>
232 </citations>
233 </tool>