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planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
author nml
date Tue, 30 Apr 2019 15:50:46 -0400
parents 930893c83a1a
children f1adc47e017a
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5:930893c83a1a 6:3c09557ac425
1 <tool id="staramr_search" name="staramr" version="@VERSION@"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@">
2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.4.0</token> 4 <token name="@VERSION@">0.5.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">staramr</requirement> 7 <requirement type="package" version="@VERSION@">staramr</requirement>
8 </requirements> 8 </requirements>
9 <version_command>staramr --version</version_command> 9 <version_command>staramr --version</version_command>
24 24
25 --nprocs "\${GALAXY_SLOTS:-1}" 25 --nprocs "\${GALAXY_SLOTS:-1}"
26 26
27 --pid-threshold $advanced.pid_threshold 27 --pid-threshold $advanced.pid_threshold
28 --percent-length-overlap-resfinder $advanced.plength_resfinder 28 --percent-length-overlap-resfinder $advanced.plength_resfinder
29 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
29 --percent-length-overlap-pointfinder $advanced.plength_pointfinder 30 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
30 31
31 $advanced.report_all_blast 32 $advanced.report_all_blast
32 $advanced.exclude_negatives 33 $advanced.exclude_negatives
33 $advanced.exclude_resistance_phenotypes 34 $advanced.exclude_resistance_phenotypes
36 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}' 37 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
37 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none' 38 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
38 --no-exclude-genes 39 --no-exclude-genes
39 #end if 40 #end if
40 41
42 #if str($advanced.plasmidfinder_type) != 'include_all'
43 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
44 #end if
45
41 --output-summary $summary 46 --output-summary $summary
47 --output-detailed-summary $detailed_summary
42 --output-resfinder $resfinder 48 --output-resfinder $resfinder
43 #if $use_pointfinder.enable 49 --output-plasmidfinder $plasmidfinder
50 #if str($use_pointfinder) != 'disabled'
44 --output-pointfinder $pointfinder 51 --output-pointfinder $pointfinder
45 #end if 52 #end if
46 --output-settings $settings 53 --output-settings $settings
47 --output-excel $excel_proper_extension 54 --output-excel $excel_proper_extension
48 55
49 --output-hits-dir staramr_hits 56 --output-hits-dir staramr_hits
50 57
51 #if $use_pointfinder.enable 58 #if str($use_pointfinder) != 'disabled'
52 --pointfinder-organism $use_pointfinder.organism 59 --pointfinder-organism '${use_pointfinder}'
53 #end if 60 #end if
54 61
55 $named_genomes 62 $named_genomes
56 ]]></command> 63 ]]></command>
57 <inputs> 64 <inputs>
58 <param type="data" name="genomes" format="fasta" multiple="true"/> 65 <param type="data" name="genomes" format="fasta" multiple="true"/>
59 <conditional name="use_pointfinder"> 66 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
60 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" /> 67 <option value="disabled" selected="true">Disable PointFinder</option>
61 <when value="true"> 68 <option value="salmonella">Salmonella</option>
62 <param name="organism" type="select" label="Select a pointfinder organism"> 69 <option value="campylobacter">Campylobacter</option>
63 <option value="salmonella" selected="true">Salmonella</option> 70 </param>
64 <option value="campylobacter">Campylobacter</option>
65 </param>
66 </when>
67 <when value="false" />
68 </conditional>
69 <section name="advanced" title="Advanced options" expanded="false"> 71 <section name="advanced" title="Advanced options" expanded="false">
70 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" 72 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
71 min="0" max="100" help="(--pid-threshold)" /> 73 min="0" max="100" help="(--pid-threshold)" />
72 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" 74 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
73 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> 75 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
74 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" 76 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
75 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> 77 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
78 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
79 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
76 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" 80 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
77 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> 81 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
78 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> 82 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
79 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> 83 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
80 <conditional name="exclude_genes"> 84 <conditional name="exclude_genes">
87 <when value="custom"> 91 <when value="custom">
88 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" /> 92 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
89 </when> 93 </when>
90 <when value="none" /> 94 <when value="none" />
91 </conditional> 95 </conditional>
96 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
97 <option value="include_all" selected="true">Include all available database types</option>
98 <option value="gram_positive">Gram Positive</option>
99 <option value="enterobacteriaceae">Enterobacteriaceae</option>
100 </param>
92 </section> 101 </section>
93 </inputs> 102 </inputs>
94 <outputs> 103 <outputs>
95 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> 104 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
105 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
96 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> 106 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
107 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
97 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> 108 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
98 <filter>use_pointfinder['enable']</filter> 109 <filter>use_pointfinder != "disabled"</filter>
99 </data> 110 </data>
100 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> 111 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
101 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> 112 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
102 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> 113 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
103 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" /> 114 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
104 </collection> 115 </collection>
105 </outputs> 116 </outputs>
106 <tests> 117 <tests>
107 <test> 118 <test>
108 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> 119 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
109 <conditional name="use_pointfinder"> 120 <param name="use_pointfinder" value="salmonella" />
110 <param name="enable" value="true" />
111 <param name="organism" value="salmonella" />
112 </conditional>
113 121
114 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> 122 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
123 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
115 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> 124 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
125 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
116 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> 126 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
117 <output_collection name="blast_hits" type="list"> 127 <output_collection name="blast_hits" type="list">
118 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> 128 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
119 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> 129 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
120 </output_collection> 130 </output_collection>
161 </tests> 171 </tests>
162 <help><![CDATA[ 172 <help><![CDATA[
163 staramr 173 staramr
164 ======= 174 =======
165 175
166 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. 176 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
167 177
168 Usage 178 Usage
169 ----- 179 -----
170 180
171 1. Select your genome contigs (in FASTA format). 181 1. Select your genome contigs (in FASTA format).
187 197
188 :: 198 ::
189 199
190 #gene_id 200 #gene_id
191 aac(6')-Iaa_1_NC_003197 201 aac(6')-Iaa_1_NC_003197
202 ColpVC_1__JX133088
192 203
193 Output 204 Output
194 ------ 205 ------
195 206
196 There are 5 different output files produced by `staramr` as well as a collection of additional files. 207 There are 5 different output files produced by `staramr` as well as a collection of additional files.
198 summary.tsv 209 summary.tsv
199 ``````````` 210 ```````````
200 211
201 A summary of all detected AMR genes/mutations in each genome, one genome per line. 212 A summary of all detected AMR genes/mutations in each genome, one genome per line.
202 213
203 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ 214 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
204 | Isolate ID | Genotype | Predicted Phenotype | 215 | Isolate ID | Genotype | Predicted Phenotype | Plasmid Genes |
205 +============+===========================================================+===========================================================================================================+ 216 +============+===========================================================+===========================================================================================================+=====================================+
206 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | 217 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
207 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ 218 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
208 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | 219 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
209 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ 220 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
221
222 detailed_summary.tsv
223 ````````````````````
224
225 A detailed summary of all detected AMR genes/mutations/plasmids in each genome, one gene per line.
226
227 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
228 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |
229 +============+=============+===================================+===========+==========+=========================+=============+========+========+===========+============+
230 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |
231 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
232 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |
233 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
234 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |
235 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
236 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |
237 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
238 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance |
239 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
240 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance |
241 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
242 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance |
243 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
244 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance |
245 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
246 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance |
247 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
248 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance |
249 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
250 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance |
251 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
252 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |
253 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
254 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |
255 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
256 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |
257 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
258 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |
259 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
260 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |
261 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
262 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |
263 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
264 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |
265 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
266
210 267
211 resfinder.tsv 268 resfinder.tsv
212 ````````````` 269 `````````````
213 270
214 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line. 271 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
230 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ 287 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
231 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 | 288 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
232 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ 289 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
233 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | 290 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
234 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ 291 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
292
293 plasmidfinder.tsv
294 `````````````````
295
296 A tabular file of each AMR plasmid gene and additional BLAST information from the **PlasmidFinder** database, one plasmid gene per line.
297
298 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
299 | Isolate ID | Gene | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
300 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
301 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
302 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
303 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
304 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
305 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 |
306 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
307 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 |
308 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
309 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 |
310 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
311 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 |
312 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
313 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 |
314 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
315 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 |
316 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
235 317
236 pointfinder.tsv 318 pointfinder.tsv
237 ``````````````` 319 ```````````````
238 320
239 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line. 321 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
252 The command-line, database versions, and other settings used to run `staramr`. 334 The command-line, database versions, and other settings used to run `staramr`.
253 335
254 :: 336 ::
255 337
256 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta 338 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
257 version = 0.2.0 339 version = 0.5.0
258 start_time = 2018-06-05 14:41:44 340 start_time = 2019-04-25 16:01:32
259 end_time = 2018-06-05 14:41:47 341 end_time = 2019-04-25 16:01:34
260 total_minutes = 0.05 342 total_minutes = 0.04
261 resfinder_db_dir = staramr/databases/data/dist/resfinder 343 resfinder_db_dir = staramr/databases/data/dist/resfinder
262 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git 344 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
263 resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2 345 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
264 resfinder_db_date = Tue, 20 Mar 2018 16:49 346 resfinder_db_date = Mon, 16 Jul 2018 16:58
265 pointfinder_db_dir = staramr/databases/data/dist/pointfinder 347 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
266 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git 348 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
267 pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a 349 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
268 pointfinder_db_date = Fri, 06 Apr 2018 09:02 350 pointfinder_db_date = Wed, 04 Jul 2018 14:27
351 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
352 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
353 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
354 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
269 pointfinder_gene_drug_version = 050218 355 pointfinder_gene_drug_version = 050218
270 resfinder_gene_drug_version = 050218 356 resfinder_gene_drug_version = 050218.1
271 357
272 results.xlsx 358 results.xlsx
273 ```````````` 359 ````````````
274 360
275 An Excel spreadsheet containing the previous 4 files as separate worksheets. 361 An Excel spreadsheet containing the previous 5 files as separate worksheets.
276 362
277 BLAST Hits 363 BLAST Hits
278 `````````` 364 ``````````
279 365
280 The dataset collection **hits** stores fasta files of the specific blast hits. 366 The dataset collection **hits** stores fasta files of the specific blast hits.
281 367
282 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada. 368 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
283 369
284 .. _staramr: https://github.com/phac-nml/staramr 370 .. _staramr: https://github.com/phac-nml/staramr
285 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db 371 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
372 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
286 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db 373 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
287 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/ 374 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
288 ]]></help> 375 ]]></help>
289 <citations> 376 <citations>
290 <citation type="bibtex"> 377 <citation type="bibtex">