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annotate srst2.xml @ 1:599a4dc309aa draft
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author | nml |
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date | Wed, 01 Mar 2017 12:39:11 -0500 |
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1 <tool id="srst2" name="SRST2" version="0.3.7"> |
0 | 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> |
3 <requirements> | |
4 <requirement type="package" version="0.1.4.6">srst2</requirement> | |
5 </requirements> | |
6 <stdio> | |
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7 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> |
0 | 8 </stdio> |
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9 <command><![CDATA[ |
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10 $__tool_directory__/srst2.pl $bam_results $scores $pileup |
0 | 11 |
12 #if $mlst_or_genedb.job_type == "mlst_only" | |
13 m $txt_results $alleles | |
14 #if ($mlst_or_genedb.allele_choice.allele_report=="all") | |
15 all | |
16 #else if ($mlst_or_genedb.allele_choice.allele_report=="new") | |
17 new | |
18 #end if | |
19 #else if $mlst_or_genedb.job_type == "custom_only" | |
20 g $genes_results $fullgenes_results | |
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21 #* |
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22 to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed |
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23 make the database names an array and then join |
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24 *# |
0 | 25 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) |
26 "$dbs" | |
27 #else if $mlst_or_genedb.job_type == "vfdb_only" | |
28 g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name | |
29 #else if $mlst_or_genedb.job_type == "mlst_custom" | |
30 b $txt_results $genes_results $fullgenes_results | |
31 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) | |
32 "$dbs" | |
33 #else if $mlst_or_genedb.job_type == "mlst_vfdb" | |
34 b $txt_results $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name | |
35 #end if | |
36 | |
37 #if $single_or_paired.type == "single" | |
38 "$single_or_paired.input_se.element_identifier" | |
39 --input_se "$input_se" | |
40 #elif $single_or_paired.type == "paired" | |
41 "$single_or_paired.forward_pe.name" | |
42 --input_pe "$single_or_paired.forward_pe" "$single_or_paired.reverse_pe" | |
43 #else | |
44 "$single_or_paired.fastq_collection.forward.name" | |
45 --input_pe "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.reverse" | |
46 #end if | |
47 | |
48 #if ($mlst_or_genedb.job_type=="mlst_only") | |
49 --mlst_db $mlst_db | |
50 --mlst_definition $mlst_defs | |
51 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
52 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
53 --report_all_consensus | |
54 #else if ($mlst_or_genedb.job_type=="mlst_vfdb") | |
55 --mlst_db $mlst_db | |
56 --mlst_definition $mlst_defs | |
57 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
58 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
59 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
60 --gene_db \$VF_PATH/${mlst_or_genedb.vfdb_in.fields.path} | |
61 #else if ($mlst_or_genedb.job_type=="mlst_custom") | |
62 --gene_db | |
63 #for $i, $database in enumerate( $mlst_or_genedb.databases ) | |
64 $database.gene_db | |
65 #end for | |
66 --mlst_db $mlst_db | |
67 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
68 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
69 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
70 --mlst_definition $mlst_defs | |
71 #else if ($mlst_or_genedb.job_type=="vfdb_only") | |
72 --gene_db \$VF_PATH/${mlst_or_genedb.vfdb_in.fields.path} | |
73 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
74 #else if ($mlst_or_genedb.job_type=="custom_only") | |
75 --gene_db | |
76 #for $i, $database in enumerate( $mlst_or_genedb.databases ) | |
77 $database.gene_db | |
78 #end for | |
79 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
80 #end if | |
81 | |
82 --read_type q | |
83 | |
84 --save_scores | |
85 | |
86 #if $options.select == "advanced" | |
87 #if $options.min_coverage | |
88 --min_coverage $options.min_coverage | |
89 #end if | |
90 #if $options.max_divergence | |
91 --max_divergence $options.max_divergence | |
92 #end if | |
93 #if $options.min_depth | |
94 --min_depth $options.min_depth | |
95 #end if | |
96 #if $options.min_edge_depth | |
97 --min_edge_depth $options.min_edge_depth | |
98 #end if | |
99 #if $options.prob_err | |
100 --prob_err $options.prob_err | |
101 #end if | |
102 #if $options.stop_after | |
103 --stop_after $options.stop_after | |
104 #end if | |
105 --other "'-p \${GALAXY_SLOTS:-1} | |
106 #if $options.maxins | |
107 --maxins $options.maxins | |
108 --minins $options.minins | |
109 #end if | |
110 '" | |
111 #if $options.mapq | |
112 --mapq $options.mapq | |
113 #end if | |
114 #if $options.baseq | |
115 --baseq $options.baseq | |
116 #end if | |
117 #else | |
118 --other "'-p \${GALAXY_SLOTS:-1}'" | |
119 #end if | |
120 | |
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121 --output \${PWD}/out |
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122 ]]></command> |
0 | 123 <inputs> |
124 <conditional name="single_or_paired"> | |
125 <param name="type" type="select" label="Read type"> | |
126 <option value="single">Single-end</option> | |
127 <option value="paired">Paired-end</option> | |
128 <option value="collection">Collection Paired-end</option> | |
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129 </param> |
0 | 130 <when value="single"> |
131 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> | |
132 </when> | |
133 <when value="paired"> | |
134 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> | |
135 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> | |
136 </when> | |
137 <when value="collection"> | |
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138 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" /> |
0 | 139 </when> |
140 </conditional> | |
141 | |
142 <conditional name="mlst_or_genedb"> | |
143 <param name="job_type" type="select" label="Job type"> | |
144 <option value="mlst_only">MLST only</option> | |
145 <option value="mlst_vfdb">MLST and VFDB</option> | |
146 <option value="mlst_custom">MLST and custom database</option> | |
147 <option value="vfdb_only">VFDB only</option> | |
148 <option value="custom_only">Custom database only</option> | |
149 </param> | |
150 <when value="mlst_only"> | |
151 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
152 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
153 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
154 <conditional name="allele_choice"> | |
155 <param name="allele_report" type="select" label="Reported Alleles" > | |
156 <option value="all">All</option> | |
157 <option value="new">Only New</option> | |
158 </param> | |
159 <when value="all"/> | |
160 <when value="new"/> | |
161 </conditional> | |
162 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
163 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
164 </param> | |
165 </when> | |
166 <when value="mlst_vfdb"> | |
167 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
168 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
169 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> | |
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170 <options from_data_table="vfdb_fasta_files" /> |
0 | 171 </param> |
172 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
173 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
174 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
175 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
176 </param> | |
177 </when> | |
178 <when value="mlst_custom"> | |
179 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
180 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
181 <repeat name="databases" title="Databases" min="1"> | |
182 <param name="gene_db" type="data" format="fasta" label="Fasta file for gene database" /> | |
183 </repeat> | |
184 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
185 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
186 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
187 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
188 </param> | |
189 </when> | |
190 <when value="vfdb_only"> | |
191 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> | |
192 <options from_data_table="vfdb_fasta_files" > | |
193 <filter type="sort_by" column="2" /> | |
194 <validator type="no_options" message="No strains are available" /> | |
195 </options> | |
196 </param> | |
197 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
198 </when> | |
199 <when value="custom_only"> | |
200 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
201 <repeat name="databases" title="Databases" min="1"> | |
202 <param name="gene_db" type="data" format="fasta" label="Fasta file for gene database" /> | |
203 </repeat> | |
204 </when> | |
205 </conditional> | |
206 <conditional name="options"> | |
207 <param name="select" type="select" label="Options Type"> | |
208 <option value="basic">Basic</option> | |
209 <option value="advanced">Advanced</option> | |
210 </param> | |
211 <when value="advanced"> | |
212 <param name="min_coverage" type="integer" label="Minimum %coverage cutoff for gene reporting" value="90"/> | |
213 <param name="max_divergence" type="integer" label="Maximum %divergence cutoff for gene reporting" value="10"/> | |
214 <param name="min_depth" type="integer" label="Minimum mean depth to flag as dubious allele call" value="5"/> | |
215 <param name="min_edge_depth" type="integer" label="Minimum edge depth to flag as dubious allele call" value="2"/> | |
216 <param name="prob_err" type="float" label="Probability of sequencing error" value="0.01"/> | |
217 <param name="stop_after" type="integer" label="Stop mapping after this number of reads have been mapped (otherwise map all)" optional="true"/> | |
218 <param name="mapq" type="integer" label="Samtools -q parameter" value="1"/> | |
219 <param name="baseq" type="integer" label="Samtools -Q parameter" value="20"/> | |
220 <param name="minins" type="integer" label="Bowtie 2 -I parameter. The minimum fragment length for valid paired-end alignments." value="0" > | |
221 <validator type="in_range" message="Must be less than -X parameter." min="0"/> | |
222 </param> | |
223 <param name="maxins" type="integer" label="Bowtie 2 -X parameter. The maximum fragment length for valid paired-end alignments." value="1000" > | |
224 <validator type="in_range" message="Must be greater than -I parameter." min="0"/> | |
225 </param> | |
226 | |
227 </when> | |
228 <when value="basic"/> | |
229 </conditional> | |
230 </inputs> | |
231 | |
232 <outputs> | |
233 <data format="bam" name="bam_results" label="Bam Results"/> | |
234 <data format="tabular" name="scores" label="Scores"/> | |
235 <data format="tabular" name="pileup" label="Pileup"/> | |
236 <data format="fasta" name="alleles" label="Alleles"> | |
237 <filter>mlst_or_genedb['job_type']=="mlst_only"</filter> | |
238 </data> | |
239 <data format="tabular" name="txt_results" label="Text Results" > | |
240 <filter>mlst_or_genedb['job_type']!="vfdb_only"</filter> | |
241 <filter>mlst_or_genedb['job_type']!="custom_only"</filter> | |
242 </data> | |
243 <data format="tabular" name="genes_results" label="Genes Results" > | |
244 <filter>mlst_or_genedb['job_type']!="mlst_only"</filter> | |
245 </data> | |
246 <data format="tabular" name="fullgenes_results" label="Full Genes Results" > | |
247 <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter> | |
248 </data> | |
249 </outputs> | |
250 | |
251 <tests> | |
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252 <test> |
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253 <param name="type" value="collection" /> |
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254 <param name="fastq_collection"> |
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255 <collection type="paired"> |
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256 <element name="forward" value="ERR028678_sampled_1.fastq" /> |
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257 <element name="reverse" value="ERR028678_sampled_2.fastq" /> |
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258 </collection> |
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259 </param> |
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260 <param name="job_type" value="mlst_only" /> |
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261 <param name="mlst_defs" value="ecoli.txt" /> |
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262 <param name="mlst_db" value="Escherichia_coli#1.fasta" /> |
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263 <param name="mlst_max_mismatch" value="10" /> |
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264 <param name="mlst_delim" value="-" /> |
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265 <output name="bam_results" file="ERR028678_sampled.bam" ftype="bam" lines_diff="2" /> |
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266 <output name="scores" file="ERR028678_sampled_scores.tabular" /> |
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267 <!-- Don't test pileup as it is too large of a file > 90 MB --> |
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268 <!-- <output name="pileup" file="ERR028678_sampled_pileup.tabular" />--> |
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269 <output name="alleles" file="ERR028678_sampled_alleles.fasta" /> |
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270 <output name="txt_results" file="ERR028678_sampled_text_results.tabular" /> |
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271 </test> |
0 | 272 </tests> |
273 | |
274 | |
275 <help> | |
276 What it does | |
277 ============ | |
278 | |
279 Short Read Sequence Typing for Bacterial Pathogens | |
280 | |
281 This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. The tool has a database of virulence factors that was extracted from http://www.mgc.ac.cn/VFs/ . | |
282 | |
283 For more information about SRST2 and for instructions on how to format custom databases, visit https://github.com/katholt/srst2 | |
284 | |
285 | |
286 Usage | |
287 ===== | |
288 | |
289 Basic Options | |
290 ------------- | |
291 | |
292 **Read Type** | |
293 - Single-end: Single end read file(s) for analysing (--input_se) | |
294 - Paired-end: Paired end read file(s) for analysing (--input_pe) | |
295 | |
296 **Job Type** | |
297 - MLST only: Reports Sequence Types | |
298 - MLST and VFDB: Reports Sequence Types and user can choose one of the built-in Virulence Factor Datebase (VFDB) strains | |
299 - MLST and custom database: Reports Sequence Types and user can upload their own custom database | |
300 - VFDB only: Use can choose one of the built-in Virulence Factor Databasse (VFDB) strains | |
301 - Custom database only: Use can upload their own custom database | |
302 | |
303 **ST definitions for MLST scheme:** | |
304 - Required if you want to calculate STs (--mlst_definitions) | |
305 | |
306 **Fasta file of MLST alleles:** | |
307 - Required if you want to calculate STs (--mlst_db) | |
308 | |
309 **Fasta file for gene database:** | |
310 - Required if you want details of the sequences. The user must provide their own database (--gene_db) | |
311 | |
312 **VFDB strain:** | |
313 - Required if you want details of the sequences. The use may choose one of the listed strains (--gene_db) | |
314 | |
315 **Read file type:** | |
316 - fastq | |
317 - solexa | |
318 - fasta | |
319 | |
320 **Character(s) separating gene name from allele number in MLST database:** | |
321 - Required for all MLST job types | |
322 - Typically either _ or - | |
323 - The output from getMLST will identify the delimiter. | |
324 | |
325 **Maximum number of mismatches per read for MLST allele calling:** | |
326 - Required for all MLST job types | |
327 - For MLST schemas with inserts this number should be set to a high value (recommended: 250) | |
328 | |
329 **Maximum number of mismatches per read for gene allele calling:** | |
330 - Required for all VDFB or custom database job types | |
331 - For genes with inserts this number should be set to a high value (recommended: 250). | |
332 | |
333 **Option Type:** | |
334 - Basic: Includes only the options listed above | |
335 - Advanced: Includes the options listed below | |
336 | |
337 ------------------------------- | |
338 | |
339 Advanced Options | |
340 ---------------- | |
341 | |
342 **Minimum %coverage cutoff for gene reporting:** | |
343 - Default is 90 (--min_coverage) | |
344 | |
345 **Maximum %divergence cutoff for gene reporting:** | |
346 - Default is 10 (--max_divergence) | |
347 | |
348 **Minimum mean depth to flag as dubious allele call:** | |
349 - Default is 5 (--min_depth) | |
350 | |
351 **Minimum edge depth to flag as dubious allele call:** | |
352 - Default is 2 (--min_edge_depth) | |
353 | |
354 **Probability of sequencing error:** | |
355 - Default is 0.01 (--prob_err) | |
356 | |
357 **Stop mapping after this number of reads have been mapped (otherwise map all):** | |
358 - Default maps all (--stop_after) | |
359 | |
360 **Other arguments to pass to bowtie2:** | |
361 --other | |
362 | |
363 **Samtools -q parameter:** | |
364 - Default is 1 (--mapq) | |
365 | |
366 **Samtools -Q parameter:** | |
367 - Default is 20 (--baseq) | |
368 | |
369 **Bowtie2 -I/--minins:** | |
370 - The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. | |
371 - The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. | |
372 - Default: 0 (essentially imposing no minimum) | |
373 | |
374 **Bowtie2 -X/--maxins:** | |
375 - The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. | |
376 - The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. | |
377 - Default: 500. | |
378 | |
379 **Acknowledgments** | |
380 Original Author: Mariam Iskander | |
381 | |
382 Jen Cabral | |
383 | |
384 Philip Mabon | |
385 | |
386 Mark Iskander | |
387 | |
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388 Eric Enns |
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389 |
0 | 390 </help> |
391 <citations> | |
392 <citation type="doi">10.1128/AAC.01310-13</citation> | |
393 </citations> | |
394 </tool> |