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comparison staramr_search.xml @ 9:61a3e97aa865 draft

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
author nml
date Mon, 30 Sep 2019 12:45:02 -0400
parents da787fc8b740
children 7573a6c11c4d
comparison
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8:da787fc8b740 9:61a3e97aa865
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