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comparison staramr_search.xml @ 13:2fd4d4c9c5c2 draft

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
author nml
date Fri, 31 Jul 2020 11:56:06 -0400
parents aeaa20b96ef2
children 4b9a8031ab74
comparison
equal deleted inserted replaced
12:aeaa20b96ef2 13:2fd4d4c9c5c2
1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy2">
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@">0.7.1</token> 4 <token name="@VERSION@">0.7.1</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>
32 32
33 --pid-threshold $advanced.pid_threshold 33 --pid-threshold $advanced.pid_threshold
34 --percent-length-overlap-resfinder $advanced.plength_resfinder 34 --percent-length-overlap-resfinder $advanced.plength_resfinder
35 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder 35 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
36 --percent-length-overlap-pointfinder $advanced.plength_pointfinder 36 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
37
38 #if str($advanced.mlst_scheme) != 'auto':
39 --mlst-scheme '${advanced.mlst_scheme}'
40 #end if
37 41
38 $advanced.report_all_blast 42 $advanced.report_all_blast
39 $advanced.exclude_negatives 43 $advanced.exclude_negatives
40 $advanced.exclude_resistance_phenotypes 44 $advanced.exclude_resistance_phenotypes
41 45
56 #if str($use_pointfinder) != 'disabled' 60 #if str($use_pointfinder) != 'disabled'
57 --output-pointfinder $pointfinder 61 --output-pointfinder $pointfinder
58 #end if 62 #end if
59 --output-settings $settings 63 --output-settings $settings
60 --output-excel $excel_proper_extension 64 --output-excel $excel_proper_extension
65 --output-mlst $mlst
61 66
62 --output-hits-dir staramr_hits 67 --output-hits-dir staramr_hits
63 68
64 #if str($use_pointfinder) != 'disabled' 69 #if str($use_pointfinder) != 'disabled'
65 --pointfinder-organism '${use_pointfinder}' 70 --pointfinder-organism '${use_pointfinder}'
95 help="(--unacceptable-number-contigs)" /> 100 help="(--unacceptable-number-contigs)" />
96 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" 101 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
97 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> 102 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
98 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> 103 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
99 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> 104 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
105 <param name="mlst_scheme" type="select" label="MLST Scheme">
106 <option value="auto" selected="true">Automatic</option>
107 <option value="abaumannii">Acinetobacter baumannii</option>
108 <option value="abaumannii_2">Acinetobacter baumannii</option>
109 <option value="achromobacter">Achromobacter </option>
110 <option value="aeromonas">Aeromonas </option>
111 <option value="afumigatus">Aspergillus afumigatus</option>
112 <option value="aphagocytophilum">Anaplasma aphagocytophilum</option>
113 <option value="arcobacter">Arcobacter </option>
114 <option value="bburgdorferi">Borrelia burgdorferi</option>
115 <option value="bcc">Burkholderia cepacia</option>
116 <option value="bcereus">Bacillus cereus</option>
117 <option value="bhampsonii">Brachyspira hampsonii</option>
118 <option value="bhenselae">Bartonella henselae</option>
119 <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>
120 <option value="bifidobacterium">Bifidobacterium bifidobacterium</option>
121 <option value="bintermedia">Brachyspira intermedia</option>
122 <option value="blicheniformis">Bacillus licheniformis</option>
123 <option value="bordetella">Bordetella pertussis</option>
124 <option value="borrelia">Borrelia </option>
125 <option value="bpilosicoli">Brachyspira pilosicoli</option>
126 <option value="bpseudomallei">Burkholderia pseudomallei</option>
127 <option value="brachyspira">Brachyspira </option>
128 <option value="bsubtilis">Bacillus subtilis</option>
129 <option value="calbicans">Candida albicans</option>
130 <option value="campylobacter">Campylobacter coli</option>
131 <option value="campylobacter">Campylobacter jejuni</option>
132 <option value="cbotulinum">Clostridium botulinum</option>
133 <option value="cconcisus">Campylobacter concisus</option>
134 <option value="cdifficile">Clostridium difficile</option>
135 <option value="cdifficile">Peptoclostridium difficile</option>
136 <option value="cdifficile_2">Clostridium difficile</option>
137 <option value="cdiphtheriae">Corynebacterium diphtheriae</option>
138 <option value="cfetus">Campylobacter fetus</option>
139 <option value="cfreundii">Citrobacter freundii</option>
140 <option value="cglabrata">Candida glabrata</option>
141 <option value="chelveticus">Campylobacter helveticus</option>
142 <option value="chlamydiales">Chlamydia </option>
143 <option value="chyointestinalis">Campylobacter hyointestinalis</option>
144 <option value="cinsulaenigrae">Campylobacter insulaenigrae</option>
145 <option value="ckrusei">Candida krusei</option>
146 <option value="clanienae">Campylobacter lanienae</option>
147 <option value="clari">Campylobacter lari</option>
148 <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option>
149 <option value="cneoformans">Cryptococcus neoformans</option>
150 <option value="cronobacter">Cronobacter </option>
151 <option value="csepticum">Clostridium septicum</option>
152 <option value="csinensis">Clonorchis sinensis</option>
153 <option value="csputorum">Campylobacter sputorum</option>
154 <option value="ctropicalis">Candida tropicalis</option>
155 <option value="cupsaliensis">Campylobacter upsaliensis</option>
156 <option value="ecloacae">Enterobacter cloacae</option>
157 <option value="ecoli">Escherichia </option>
158 <option value="ecoli">Shigella </option>
159 <option value="ecoli_2">Escherichia </option>
160 <option value="edwardsiella">Edwardsiella tarda</option>
161 <option value="efaecalis">Enterococcus faecalis</option>
162 <option value="efaecium">Enterococcus faecium</option>
163 <option value="fpsychrophilum">Flavobacterium psychrophilum</option>
164 <option value="haemophilus">Haemophilus </option>
165 <option value="hcinaedi">Helicobacter cinaedi</option>
166 <option value="hinfluenzae">Haemophilus influenzae</option>
167 <option value="hparasuis">Haemophilus parasuis</option>
168 <option value="hpylori">Helicobacter pylori</option>
169 <option value="hsuis">Haematopinus suis</option>
170 <option value="kkingae">Kingella kingae</option>
171 <option value="koxytoca">Klebsiella oxytoca</option>
172 <option value="kpneumoniae">Klebsiella pneumoniae</option>
173 <option value="kseptempunctata">Kudoa septempunctata</option>
174 <option value="lcasei">Lactobacillus casei</option>
175 <option value="legionella">Legionella </option>
176 <option value="leptospira">Leptospira </option>
177 <option value="leptospira_2">Leptospira </option>
178 <option value="leptospira_3">Leptospira </option>
179 <option value="lmonocytogenes">Listeria monocytogenes</option>
180 <option value="lsalivarius">Lactobacillus salivarius</option>
181 <option value="mabscessus">Mycobacterium abscessus</option>
182 <option value="magalactiae">Mycoplasma agalactiae</option>
183 <option value="mbovis">Mycoplasma bovis</option>
184 <option value="mcatarrhalis">Moraxells catarrhalis</option>
185 <option value="mhaemolytica">Mannheimia haemolytica</option>
186 <option value="mhyorhinis">Mycoplasma hyorhinis</option>
187 <option value="mmassiliense">Mycobacterium massiliense</option>
188 <option value="mplutonius">Melissococcus plutonius</option>
189 <option value="neisseria">Neisseria </option>
190 <option value="orhinotracheale">Ornithobacterium rhinotracheale</option>
191 <option value="otsutsugamushi">Orientia tsutsugamushi</option>
192 <option value="pacnes">Propionibacterium acnes</option>
193 <option value="paeruginosa">Pseudomonas aeruginosa</option>
194 <option value="pagglomerans">Pantoea agglomerans</option>
195 <option value="pfluorescens">Pseudomonas fluorescens</option>
196 <option value="pfreudenreichii">Propionibacterium freudenreichii</option>
197 <option value="pgingivalis">Porphyromonas gingivalis</option>
198 <option value="plarvae">Paenibacillus larvae</option>
199 <option value="pmultocida_multihost">Pasteurella multocida</option>
200 <option value="pmultocida_rirdc">Pasteurella multocida</option>
201 <option value="ppentosaceus">Pediococcus pentosaceus</option>
202 <option value="pshigelloides">Plesiomonas shigelloides</option>
203 <option value="ranatipestifer">Riemerella anatipestifer</option>
204 <option value="sagalactiae">Streptococcus agalactiae</option>
205 <option value="saureus">Staphylococcus aureus</option>
206 <option value="scanis">Streptococcus canis</option>
207 <option value="sdysgalactiae">Streptococcus dysgalactiae</option>
208 <option value="senterica">Salmonella enterica</option>
209 <option value="sepidermidis">Staphylococcus epidermidis</option>
210 <option value="sgallolyticus">Streptococcus gallolyticus</option>
211 <option value="shaemolyticus">Staphylococcus haemolyticus</option>
212 <option value="shominis">Stapylococcus hominis</option>
213 <option value="sinorhizobium">Sinorhizobium </option>
214 <option value="slugdunensis">Staphylococcus lugdunensis</option>
215 <option value="smaltophilia">Stenotrophomonas maltophilia</option>
216 <option value="soralis">Streptococcus oralis</option>
217 <option value="spneumoniae">Streptococcus pneumoniae</option>
218 <option value="spseudintermedius">Staphylococcus pseudintermedius</option>
219 <option value="spyogenes">Streptococcus pyogenes</option>
220 <option value="ssuis">Streptococcus suis</option>
221 <option value="sthermophilus">Streptococcus thermophilus</option>
222 <option value="sthermophilus_2">Streptococcus thermophilus</option>
223 <option value="streptomyces">Streptomyces </option>
224 <option value="suberis">Streptococcus uberis</option>
225 <option value="szooepidemicus">Streptococcus equi</option>
226 <option value="taylorella">Taylorella </option>
227 <option value="tenacibaculum">Tenacibaculum </option>
228 <option value="tvaginalis">Trichomonas vaginalis</option>
229 <option value="vcholerae">Vibrio cholerae</option>
230 <option value="vibrio">Vibrio </option>
231 <option value="vparahaemolyticus">Vibrio parahaemolyticus</option>
232 <option value="vtapetis">Vibrio tapetis</option>
233 <option value="vvulnificus">Vibrio vulnificus</option>
234 <option value="wolbachia">Wolbachia </option>
235 <option value="xfastidiosa">Xylella fastidiosa</option>
236 <option value="yersinia">Yersinia </option>
237 <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option>
238 <option value="yruckeri">Yersinia ruckeri</option>
239 </param>
100 <conditional name="exclude_genes"> 240 <conditional name="exclude_genes">
101 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results"> 241 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
102 <option value="default" selected="true">Exclude default list of AMR genes</option> 242 <option value="default" selected="true">Exclude default list of AMR genes</option>
103 <option value="custom">Provide a custom list of AMR genes to exclude</option> 243 <option value="custom">Provide a custom list of AMR genes to exclude</option>
104 <option value="none">Do not exclude any AMR genes</option> 244 <option value="none">Do not exclude any AMR genes</option>
115 <option value="enterobacteriaceae">Enterobacteriaceae</option> 255 <option value="enterobacteriaceae">Enterobacteriaceae</option>
116 </param> 256 </param>
117 </section> 257 </section>
118 </inputs> 258 </inputs>
119 <outputs> 259 <outputs>
120 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> 260 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
121 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> 261 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
122 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> 262 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
123 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> 263 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
124 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> 264 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
125 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> 265 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
132 </collection> 272 </collection>
133 </outputs> 273 </outputs>
134 <tests> 274 <tests>
135 <test> 275 <test>
136 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> 276 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
137 <param name="use_pointfinder" value="salmonella" /> 277 <param name="use_pointfinder" value="salmonella" />
138 278
139 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> 279 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
140 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> 280 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
141 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> 281 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
142 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> 282 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
155 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> 295 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
156 </output_collection> 296 </output_collection>
157 </test> 297 </test>
158 <test> 298 <test>
159 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> 299 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
300 <section name="advanced">
301 <param name="mlst_scheme" value="kpneumoniae" />
302 </section>
303 <output name="mlst" file="mlst.tsv" ftype="tabular" />
304 </test>
305 <test>
306 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
160 <param name="pid_threshold" value="99.8" /> 307 <param name="pid_threshold" value="99.8" />
161 308
162 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> 309 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
163 </test> 310 </test>
164 <test> 311 <test>
247 summary.tsv 394 summary.tsv
248 ``````````` 395 ```````````
249 396
250 A summary of all detected AMR genes/mutations in each genome, one genome per line. 397 A summary of all detected AMR genes/mutations in each genome, one genome per line.
251 398
399 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
252 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback | 400 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
253 |------------|----------------|-----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------|-------------------------------------|-----------|---------------|---------------|-----------|---------------------------------------------------|-------------------------| 401 +============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+
254 | SRR1952908 | Passed | 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 | senterica | 11 | 4796082 | 225419 | 59 | | 402 | SRR1952908 | Passed | 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 | senterica | 11 | 4796082 | 225419 | 59 | |
403 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
255 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | | 404 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | |
405 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
256 406
257 407
258 detailed_summary.tsv 408 detailed_summary.tsv
259 ```````````````````` 409 ````````````````````
260 410