Mercurial > repos > nml > staramr
comparison staramr_search.xml @ 9:61a3e97aa865 draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
author | nml |
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date | Mon, 30 Sep 2019 12:45:02 -0400 |
parents | da787fc8b740 |
children | 7573a6c11c4d |
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8:da787fc8b740 | 9:61a3e97aa865 |
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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, PlasmidFinder, 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@">0.5.1</token> | 4 <token name="@VERSION@">0.6.1</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> |
99 <option value="enterobacteriaceae">Enterobacteriaceae</option> | 99 <option value="enterobacteriaceae">Enterobacteriaceae</option> |
100 </param> | 100 </param> |
101 </section> | 101 </section> |
102 </inputs> | 102 </inputs> |
103 <outputs> | 103 <outputs> |
104 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> | |
104 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> | 105 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> |
105 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> | 106 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> |
106 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> | 107 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> |
107 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> | 108 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> |
108 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> | 109 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> |
115 </collection> | 116 </collection> |
116 </outputs> | 117 </outputs> |
117 <tests> | 118 <tests> |
118 <test> | 119 <test> |
119 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 120 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> |
120 <param name="use_pointfinder" value="salmonella" /> | 121 <param name="use_pointfinder" value="salmonella" /> |
121 | 122 |
122 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> | 123 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> |
123 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> | 124 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> |
124 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> | 125 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> |
125 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> | 126 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> |
202 ColpVC_1__JX133088 | 203 ColpVC_1__JX133088 |
203 | 204 |
204 Output | 205 Output |
205 ------ | 206 ------ |
206 | 207 |
207 There are 5 different output files produced by `staramr` as well as a collection of additional files. | 208 There are 6 different output files produced by `staramr` as well as a collection of additional files. |
209 | |
210 mlst.tsv | |
211 ```````````````````` | |
212 | |
213 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. | |
214 | |
215 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ | |
216 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 | | |
217 +============+==============+===================================+============+============+============+============+============+============+============+ | |
218 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | | |
219 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+ | |
220 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | | |
221 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ | |
222 | |
208 | 223 |
209 summary.tsv | 224 summary.tsv |
210 ``````````` | 225 ``````````` |
211 | 226 |
212 A summary of all detected AMR genes/mutations in each genome, one genome per line. | 227 A summary of all detected AMR genes/mutations in each genome, one genome per line. |
334 The command-line, database versions, and other settings used to run `staramr`. | 349 The command-line, database versions, and other settings used to run `staramr`. |
335 | 350 |
336 :: | 351 :: |
337 | 352 |
338 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta | 353 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta |
339 version = 0.5.1 | 354 version = 0.6.1 |
340 start_time = 2019-04-25 16:01:32 | 355 start_time = 2019-04-25 16:01:32 |
341 end_time = 2019-04-25 16:01:34 | 356 end_time = 2019-04-25 16:01:34 |
342 total_minutes = 0.04 | 357 total_minutes = 0.04 |
343 resfinder_db_dir = staramr/databases/data/dist/resfinder | 358 resfinder_db_dir = staramr/databases/data/dist/resfinder |
344 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git | 359 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git |