Mercurial > repos > estrain > amrfinderplus_db

comparison amrfinderplus_db.xml @ 0:06165bd8c9a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8
author estrain
date Thu, 12 Mar 2026 18:53:36 +0000
parents
children ea95be45d908
comparison
equal deleted inserted replaced
-1:000000000000 0:06165bd8c9a0
1 <tool id="amrfinderplus_db" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 NCBI Antimicrobial Resistance Gene Finder
4 </description>
5 <macros>
6 <import>macro.xml</import>
7 </macros>
8 <expand macro="biotools"/>
9 <expand macro="requirements"/>
10 <expand macro="version_command"/>
11 <command detect_errors="aggressive"><![CDATA[
12 amrfinder
13 #*======================================
14 CPU option
15 ======================================*#
16 --threads \${GALAXY_SLOTS:-1}
17 #*======================================
18 DATABASE
19 ======================================*#
20 --database '$input_option.amrfinder_db_select.fields.path'
21 #*======================================
22 INPUT TYPE
23 ======================================*#
24 #if $input_option.input_mode.input_select == 'nucleotide'
25 --nucleotide $input_option.input_mode.nucleotide_input
26 #if $input_option.input_mode.nucleotide_flank5_size > 0
27 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
28 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
29 #end if
30 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
31 #elif $input_option.input_mode.input_select == 'protein'
32 --protein $input_option.input_mode.protein_input
33 #if $input_option.input_mode.gff_annotation
34 --gff $input_option.input_mode.gff_annotation
35 #end if
36 #if $input_option.input_mode.annotation_format
37 --annotation_format $input_option.input_mode.annotation_format
38 #end if
39 --protein_output 'amrfinderplus_protein_output.fasta'
40 #else
41 --nucleotide $input_option.input_mode.nucleotide_input
42 #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
43 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
44 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
45 #end if
46 --protein $input_option.input_mode.protein_input
47 --gff $input_option.input_mode.gff_annotation
48 --annotation_format $input_option.input_mode.annotation_format
49 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
50 --protein_output 'amrfinderplus_protein_output.fasta'
51 #end if
52 #*======================================
53 ORGANISM PART
54 ======================================*#
55 #if $organism_options.organism_conditionnal.organism_select
56 --organism '$organism_options.organism_conditionnal.organism'
57 #if $organism_options.organism_conditionnal.mutation_all
58 $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv'
59 #end if
60 #if $options.plus
61 $organism_options.organism_conditionnal.report_common
62 #end if
63 #end if
64 #*======================================
65 OPTIONS
66 ======================================*#
67 --ident_min '$options.ident_min'
68 --coverage_min '$options.coverage_min'
69 #if '$options.translation_table'
70 --translation_table '$options.translation_table'
71 #end if
72 #if '$options.name'
73 --name '$options.name'
74 #end if
75 $options.plus
76 $options.report_all_equal
77 $options.print_node
78 --output 'amrfinderplus_report.tsv'
79
80 ]]></command>
81 <inputs>
82
83 <section name="input_option" title="Input/Output options" expanded="true">
84 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
85 <options from_data_table="amrfinderplus_versioned_database">
86 </options>
87 </param>
88 <conditional name="input_mode">
89 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)">
90 <option value="nucleotide">Nucleotide</option>
91 <option value="protein">Protein</option>
92 <option value="nucl_prot">Nucleotide and Protein</option>
93 </param>
94 <when value="nucleotide">
95 <expand macro="nucl_input" option="false"/>
96 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
97 </when>
98 <when value="protein">
99 <expand macro="prot_input" option="false"/>
100 <expand macro="annotation_type" option="true"/>
101 </when>
102 <when value="nucl_prot">
103 <expand macro="nucl_input" option="false"/>
104 <expand macro="prot_input" option="false"/>
105 <expand macro="annotation_type" option="false"/>
106 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
107 </when>
108 </conditional>
109 </section>
110 <!-- ORGANISM OPTIONS -->
111 <section name="organism_options" title="Organism options">
112 <conditional name="organism_conditionnal">
113 <param name="organism_select" type="select" label="Add organism specifications">
114 <option value="" selected="true">No specifications</option>
115 <option value="add_organism">Add organism specifications</option>
116 </param>
117 <when value="add_organism">
118 <param argument="--organism" type="select" optional="false" label="Taxonomy group point mutation" help="Choose a taxonomic group to point mutation screening">
119 <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option>
120 <option value="Burkholderia_cepacia">Burkholderia_cepacia</option>
121 <option value="Burkholderia_pseudomallei">Burkholderia_pseudomallei</option>
122 <option value="Campylobacter">Campylobacter</option>
123 <option value="Citrobacter_freundii">Citrobacter_freundii</option>
124 <option value="Clostridioides_difficile">Clostridioides_difficile</option>
125 <option value="Enterobacter_cloacae">Enterobacter_cloacae</option>
126 <option value="Enterococcus_faecalis">Enterococcus_faecalis</option>
127 <option value="Enterococcus_faecium">Enterococcus_faecium</option>
128 <option value="Escherichia">Escherichia</option>
129 <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option>
130 <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option>
131 <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option>
132 <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option>
133 <option value="Neisseria_meningitidis">Neisseria_meningitidis</option>
134 <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option>
135 <option value="Salmonella">Salmonella</option>
136 <option value="Serratia_marcescens">Serratia_marcescens</option>
137 <option value="Staphylococcus_aureus">Staphylococcus_aureus</option>
138 <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option>
139 <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option>
140 <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option>
141 <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option>
142 <option value="Vibrio_cholerae">Vibrio_cholerae</option>
143 </param>
144 <param argument="--mutation_all" type="boolean" truevalue="--mutation_all" falsevalue="" label="Report genotypes at all locations screened for point mutations"/>
145 <param argument="--report_common" type="boolean" truevalue="--report_common" falsevalue=""
146 label="Report proteins common to a taxonomy group (need the plus and organism options)"/>
147 </when>
148 <when value="">
149 </when>
150 </conditional>
151 </section>
152 <!-- OPTIONS -->
153 <section name="options" title="Options">
154 <param argument="--ident_min" type="float" min="-1" max="1" value="-1" label="Minimum identity"
155 help="Minimum proportion of identical amino acids in alignment. -1 means use a curated threshold if it exists and 0.9 otherwise (default: -1)"/>
156 <param argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage"
157 help="Minimum coverage of the reference protein (0 to 1, default: 0.5)"/>
158 <param argument="--translation_table" type="select" optional="true" label="Translation table" help="NCBI genetic code for translated BLAST (default: bacterial table 11)">
159 <option value="1">1 Standard code</option>
160 <option value="2">2 Vertebrate mitochondrial</option>
161 <option value="3">3 Yeast mitochondrial</option>
162 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
163 <option value="5">5 Invertebrate mitochondrial</option>
164 <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
165 <option value="9">9 Echinoderm and flatworm mitochondrial</option>
166 <option value="10">10 Euplotid nuclear</option>
167 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
168 <option value="12">12 Alternative yeast nuclear</option>
169 <option value="13">13 Ascidian mitochondrial</option>
170 <option value="14">14 Alternative flatworm mitochondrial</option>
171 <option value="16">16 Chlorophycean mitochondrial</option>
172 <option value="21">21 Trematode Mitochondrial</option>
173 <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
174 <option value="23">23 Thraustochytrium Mitochondrial</option>
175 <option value="24">24 Rhabdopleuridae Mitochondrial</option>
176 <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
177 <option value="26">26 Pachysolen tannophilus Nuclear</option>
178 <option value="27">27 Karyorelict Nuclear</option>
179 <option value="28">28 Condylostoma Nuclear</option>
180 <option value="29">29 Mesodinium nuclear</option>
181 <option value="30">30 Peritrich nuclear</option>
182 <option value="31">31 Blastocrithidia nuclear</option>
183 <option value="33">33 Cephalodiscidae mitochondrial</option>
184 </param>
185 <param argument="--plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/>
186 <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/>
187 <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/>
188 <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/>
189 </section>
190 </inputs>
191 <outputs>
192 <data name="amrfinderplus_report" format="tabular" from_work_dir="amrfinderplus_report.tsv" label="${tool.name} on ${on_string}: AMRFinderPlus report"/>
193 <data name="mutation_all_report" format="tabular" from_work_dir="mutation_all_report.tsv" label="${tool.name} on ${on_string}: Point mutation report">
194 <filter> organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True </filter>
195 </data>
196 <data name="protein_output" format="fasta" from_work_dir="amrfinderplus_protein_output.fasta" label="${tool.name} on ${on_string}: Protein identified sequences">
197 <filter> input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']</filter>
198 </data>
199 <data name="nucleotide_output" format="fasta" from_work_dir="amrfinderplus_nucleotide_output.fasta" label="${tool.name} on ${on_string}: Nucleotide identified sequences">
200 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] </filter>
201 </data>
202 <data name="nucleotide_flank5_output" format="fasta" from_work_dir="amrfinderplus_flanking_sequence_output.fasta"
203 label="${tool.name} on ${on_string}: Nucleotide sequences with 5' flanking regions">
204 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0 </filter>
205 </data>
206 </outputs>
207 <tests>
208 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input -->
209 <section name="input_option">
210 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
211 <conditional name="input_mode">
212 <param name="input_select" value="nucleotide"/>
213 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
214 </conditional>
215 </section>
216 <output name="amrfinderplus_report" ftype="tabular">
217 <assert_contents>
218 <has_n_columns n="22"/>
219 <has_n_lines n="8"/>
220 <has_text text="optrA"/>
221 <has_text text="WP_063854496"/>
222 <has_text text="WP_063843211"/>
223 </assert_contents>
224 </output>
225 <output name="nucleotide_output" ftype="fasta">
226 <assert_contents>
227 <has_n_lines n="142"/>
228 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
229 <has_text text="TTGTCCAAAGCC"/>
230 </assert_contents>
231 </output>
232 </test>
233 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options -->
234 <section name="input_option">
235 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
236 <conditional name="input_mode">
237 <param name="input_select" value="nucleotide"/>
238 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
239 <param name="nucleotide_flank5_size" value="150"/>
240 </conditional>
241 </section>
242 <section name="organism_options">
243 <conditional name="organism_conditionnal">
244 <param name="organism_select" value="add_organism"/>
245 <param name="organism" value="Enterococcus_faecalis"/>
246 <param name="report_common" value="true"/>
247 </conditional>
248 </section>
249 <section name="options">
250 <param name="ident_min" value="0.1"/>
251 <param name="coverage_min" value="0.1"/>
252 <param name="translation_table" value="11"/>
253 <param name="plus" value="true"/>
254 <param name="report_all_equal" value="true"/>
255 <param name="print_node" value="true"/>
256 <param name="name" value="test_2"/>
257 <param name="log" value="true"/>
258 </section>
259 <output name="amrfinderplus_report" ftype="tabular">
260 <assert_contents>
261 <has_n_columns n="24"/>
262 <has_n_lines n="13"/>
263 <has_text text="optrA"/>
264 <has_text text="WP_063854496"/>
265 </assert_contents>
266 </output>
267 <output name="nucleotide_output" ftype="fasta">
268 <assert_contents>
269 <has_n_lines n="267"/>
270 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
271 <has_text text="TTGTCCAAAGCC"/>
272 </assert_contents>
273 </output>
274 <output name="nucleotide_flank5_output" ftype="fasta">
275 <assert_contents>
276 <has_n_lines n="298"/>
277 <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
278 <has_text text="TTGTCCAAAGCC"/>
279 </assert_contents>
280 </output>
281 </test>
282 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options -->
283 <section name="input_option">
284 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
285 <conditional name="input_mode">
286 <param name="input_select" value="nucleotide"/>
287 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
288 </conditional>
289 </section>
290 <section name="organism_options">
291 <conditional name="organism_conditionnal">
292 <param name="organism_select" value="add_organism"/>
293 <param name="organism" value="Enterococcus_faecalis"/>
294 <param name="report_common" value="true"/>
295 </conditional>
296 </section>
297 <section name="options">
298 <param name="report_all_equal" value="true"/>
299 </section>
300 <output name="amrfinderplus_report" ftype="tabular">
301 <assert_contents>
302 <has_n_columns n="22"/>
303 <has_n_lines n="9"/>
304 <has_text text="optrA"/>
305 <has_text text="WP_063854496"/>
306 <has_text text="WP_063856080"/>
307 </assert_contents>
308 </output>
309 <output name="nucleotide_output" ftype="fasta">
310 <assert_contents>
311 <has_n_lines n="142"/>
312 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
313 <has_text text="TTGTCCAAAGCC"/>
314 </assert_contents>
315 </output>
316 </test>
317 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input -->
318 <section name="input_option">
319 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
320 <conditional name="input_mode">
321 <param name="input_select" value="protein"/>
322 <param name="protein_input" value="enterococcus_faecalis.faa"/>
323 </conditional>
324 </section>
325 <output name="amrfinderplus_report" ftype="tabular">
326 <assert_contents>
327 <has_n_columns n="18"/>
328 <has_n_lines n="7"/>
329 <has_text text="optrA"/>
330 <has_text text="WP_063854496"/>
331 <has_text text="WP_063856080"/>
332 </assert_contents>
333 </output>
334 <output name="protein_output" ftype="fasta">
335 <assert_contents>
336 <has_n_lines n="49"/>
337 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
338 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
339 </assert_contents>
340 </output>
341 </test>
342 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta -->
343 <section name="input_option">
344 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
345 <conditional name="input_mode">
346 <param name="input_select" value="protein"/>
347 <param name="protein_input" value="enterococcus_faecalis.faa"/>
348 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
349 <param name="annotation_format" value="bakta"/>
350 </conditional>
351 </section>
352 <section name="organism_options">
353 <conditional name="organism_conditionnal">
354 <param name="organism_select" value="add_organism"/>
355 <param name="organism" value="Enterococcus_faecalis"/>
356 <param name="report_common" value="true"/>
357 </conditional>
358 </section>
359 <section name="options">
360 <param name="ident_min" value="0.1"/>
361 <param name="coverage_min" value="0.4"/>
362 <param name="translation_table" value="11"/>
363 <param name="plus" value="true"/>
364 <param name="report_all_equal" value="true"/>
365 <param name="print_node" value="true"/>
366 <param name="name" value="test_5"/>
367 </section>
368 <output name="amrfinderplus_report" ftype="tabular">
369 <assert_contents>
370 <has_n_columns n="24"/>
371 <has_n_lines n="8"/>
372 <has_text text="optrA"/>
373 <has_text text="IDOBJL_14770"/>
374 <has_text text="WP_063856080"/>
375 </assert_contents>
376 </output>
377 <output name="nucleotide_output" ftype="fasta">
378 <assert_contents>
379 <has_n_lines n="49"/>
380 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
381 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
382 </assert_contents>
383 </output>
384 </test>
385 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation -->
386 <section name="input_option">
387 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
388 <conditional name="input_mode">
389 <param name="input_select" value="protein"/>
390 <param name="protein_input" value="PROKKA_05252023.faa"/>
391 <param name="gff_annotation" value="PROKKA_05252023.gff"/>
392 <param name="annotation_format" value="prokka"/>
393 </conditional>
394 </section>
395 <output name="amrfinderplus_report" ftype="tabular">
396 <assert_contents>
397 <has_n_columns n="22"/>
398 <has_n_lines n="7"/>
399 <has_text text="FODBOAIN_02586"/>
400 <has_text text="WP_063856395"/>
401 </assert_contents>
402 </output>
403 <output name="protein_output" ftype="fasta">
404 <assert_contents>
405 <has_n_lines n="49"/>
406 <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/>
407 <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/>
408 </assert_contents>
409 </output>
410 </test>
411 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation -->
412 <section name="input_option">
413 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
414 <conditional name="input_mode">
415 <param name="input_select" value="protein"/>
416 <param name="protein_input" value="input_ncbi.faa"/>
417 <param name="gff_annotation" value="annotation_ncbi.gff3"/>
418 </conditional>
419 </section>
420 <output name="amrfinderplus_report" ftype="tabular">
421 <assert_contents>
422 <has_n_columns n="22"/>
423 <has_n_lines n="4"/>
424 <has_text text="blaOXA"/>
425 <has_text text="WP_063855540"/>
426 </assert_contents>
427 </output>
428 <output name="protein_output" ftype="fasta">
429 <assert_contents>
430 <has_n_lines n="17"/>
431 <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/>
432 <has_text text="SSNPDAAPVSS"/>
433 </assert_contents>
434 </output>
435 </test>
436 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input -->
437 <section name="input_option">
438 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
439 <conditional name="input_mode">
440 <param name="input_select" value="nucl_prot"/>
441 <param name="protein_input" value="enterococcus_faecalis.faa"/>
442 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
443 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
444 <param name="annotation_format" value="bakta"/>
445 </conditional>
446 </section>
447 <section name="organism_options">
448 <conditional name="organism_conditionnal">
449 <param name="organism_select" value="add_organism"/>
450 <param name="organism" value="Enterococcus_faecalis"/>
451 </conditional>
452 </section>
453 <output name="amrfinderplus_report" ftype="tabular">
454 <assert_contents>
455 <has_n_columns n="22"/>
456 <has_n_lines n="8"/>
457 <has_text text="IDOBJL_14770"/>
458 <has_text text="WP_063856080"/>
459 </assert_contents>
460 </output>
461 <output name="nucleotide_output" ftype="fasta">
462 <assert_contents>
463 <has_n_lines n="143"/>
464 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
465 <has_text text="CTTATCTGTATAG"/>
466 </assert_contents>
467 </output>
468 <output name="protein_output" ftype="fasta">
469 <assert_contents>
470 <has_n_lines n="37"/>
471 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
472 <has_text text="QEAGAGMSLLNFT"/>
473 </assert_contents>
474 </output>
475 </test>
476 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results -->
477 <section name="input_option">
478 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
479 <conditional name="input_mode">
480 <param name="input_select" value="nucl_prot"/>
481 <param name="protein_input" value="e_faecalis_rast.faa"/>
482 <param name="nucleotide_input" value="e_faecalis_rast.fna"/>
483 <param name="gff_annotation" value="e_faecalis_rast.gff"/>
484 <param name="annotation_format" value="rast"/>
485 </conditional>
486 </section>
487 <section name="organism_options">
488 <conditional name="organism_conditionnal">
489 <param name="organism_select" value="add_organism"/>
490 <param name="organism" value="Enterococcus_faecalis"/>
491 <param name="mutation_all" value="true"/>
492 </conditional>
493 </section>
494 <section name="options">
495 <param name="ident_min" value="0.1"/>
496 <param name="coverage_min" value="0.1"/>
497 <param name="plus" value="true"/>
498 <param name="print_node" value="true"/>
499 <param name="name" value="test_5"/>
500 </section>
501 <output name="amrfinderplus_report" ftype="tabular">
502 <assert_contents>
503 <has_n_columns n="24"/>
504 <has_n_lines n="2"/>
505 <has_text text="MUPIROCIN"/>
506 <has_text text="WP_063854488"/>
507 </assert_contents>
508 </output>
509 <output name="nucleotide_output" ftype="fasta">
510 <assert_contents>
511 <has_n_lines n="40"/>
512 <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
513 <has_text text="ATCAGTCGTGAAATAGAA"/>
514 </assert_contents>
515 </output>
516 <output name="protein_output" ftype="fasta">
517 <assert_contents>
518 <has_n_lines n="0"/>
519 </assert_contents>
520 </output>
521 <output name="mutation_all_report" ftype="tabular">
522 <assert_contents>
523 <has_n_columns n="24"/>
524 <has_n_lines n="5"/>
525 <has_text text="23S_GA375AG"/>
526 <has_text text="NZ_CP04"/>
527 </assert_contents>
528 </output>
529 </test>
530 </tests>
531 <help><![CDATA[
532 **What it does**
533
534 AMRFinderPlus is a tool to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.
535
536 **Input file analysis**
537
538 AMRFinderPlus can check in nucleotide and/or protein fasta file
539 When protein file is provided, sensitivity is higher if you add an annotation file
540
541 **Organism options**
542
543 With organism informations AMRFinderPlus screens known resistance causing point mutations and blacklisting of common, non-informative genes.
544
545 The **mutation_all** option make a new output file containing all detected variants from the reference sequence.
546
547 This file allows you to distinguish between called point mutations that were the sensitive variant and the point mutations that could not be called because the sequence was not found.
548
549 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
550 | Organism option | Point mutations | Blacklisted plus genes | Notes |
551 +=================================+==================+=============================+============================================================+
552 | Acinetobacter_baumannii | X | | Use for the A. baumannii-calcoaceticus species complex |
553 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
554 | Burkholderia_cepacia | X | | Use for the Burkholderia cepacia species complex |
555 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
556 | Burkholderia_pseudomallei | X | | Use for the Burkholderia pseudomallei species complex |
557 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
558 | Campylobacter | X | | Use for C. coli and C. jejuni |
559 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
560 | Citrobacter_freundii | X | | |
561 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
562 | Clostridioides_difficile | X | | |
563 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
564 | Enterobacter_cloacae | X | | |
565 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
566 | Enterococcus_faecalis | X | | |
567 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
568 | Enterococcus_faecium | X | | Use for E. hirae |
569 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
570 | Escherichia | X | X | Use for Shigella and Escherichia |
571 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
572 | Klebsiella_oxytoca | X | X | |
573 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
574 | Klebsiella_pneumoniae | X | X | Use for K. pneumoniae species complex and K. aerogenes |
575 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
576 | Neisseria_gonorrhoeae | X | | |
577 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
578 | Neisseria_meningitidis | X | | |
579 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
580 | Pseudomonas_aeruginosa | X | | |
581 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
582 | Salmonella | X | X | |
583 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
584 | Serratia_marcescens | X | | |
585 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
586 | Staphylococcus_aureus | X | | |
587 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
588 | Staphylococcus_pseudintermedius | X | X | |
589 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
590 | Streptococcus_agalactiae | X | | |
591 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
592 | Streptococcus_pneumoniae | X | | Use for S. pneumoniae and S. mitis |
593 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
594 | Streptococcus_pyogenes | X | | |
595 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
596 | Vibrio_cholerae | X | | |
597 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
598
599
600 **Supplementary options**
601 - *nucleotide 5' flanking size* to extract nucleotide matches and a range of nucleotide in 5'
602 - *Minimum identity* to choose threshold in amino acids alignemnt. -1 for a high curation threshold.
603 - *Minimum coverage* Coverage to protein alignment.
604 - *Translation table* by default AMRFinderPlus work on bacteria but can be modified to some other Phyla.
605 - *Plus* option provide more information related to virulence, stress response ...
606
607 **Output files**
608
609 AMRFinderPlus can generate some differents files :
610 - The AMRFinderPlus report with identified protein, gene and AMR related informations.
611 - A report with all detected variants from the reference sequence.
612 - The protein and/ort nucleotide matched sequences.
613 - Only when nucleotide a nucleotide fasta file could be provided with 5' flanking regions.
614
615
616 ]]></help>
617 <expand macro="citations"/>
618 </tool>