Mercurial > repos > nml > staramr
comparison staramr_search.xml @ 15:be818ae858e4 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
author | nml |
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date | Wed, 22 Jun 2022 14:44:55 +0000 |
parents | 4b9a8031ab74 |
children | 4d83eccf5f81 |
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14:4b9a8031ab74 | 15:be818ae858e4 |
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1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0"> | 1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> |
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@">0.7.2</token> | 4 <token name="@VERSION@">0.8.0</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 <!-- The staramr conda package includes the mlst software, but the list of schemes | |
9 changes depending on the version. I specify the exact version here to make sure | |
10 the list of schemes provided is consistent --> | |
11 <requirement type="package" version="2.22.0">mlst</requirement> | |
8 </requirements> | 12 </requirements> |
9 <version_command>staramr --version</version_command> | 13 <version_command>staramr --version</version_command> |
10 <command detect_errors="exit_code"><![CDATA[ | 14 <command detect_errors="exit_code"><![CDATA[ |
11 #import re | 15 #import re |
12 | 16 |
15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) | 19 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) |
16 ln -s '$genome' $_named_genome && | 20 ln -s '$genome' $_named_genome && |
17 #set $named_genomes = $named_genomes + ' ' + $_named_genome | 21 #set $named_genomes = $named_genomes + ' ' + $_named_genome |
18 #end for | 22 #end for |
19 | 23 |
20 #set $excel_proper_extension = '"results.xlsx"' | 24 #set $excel_proper_extension = 'results.xlsx' |
21 ln -s "$excel" $excel_proper_extension && | 25 ln -s '$excel' $excel_proper_extension && |
22 | 26 |
23 staramr search | 27 staramr search |
24 | 28 |
25 --nprocs "\${GALAXY_SLOTS:-1}" | 29 --nprocs "\${GALAXY_SLOTS:-1}" |
26 | 30 |
51 | 55 |
52 #if str($advanced.plasmidfinder_type) != 'include_all' | 56 #if str($advanced.plasmidfinder_type) != 'include_all' |
53 --plasmidfinder-database-type '${advanced.plasmidfinder_type}' | 57 --plasmidfinder-database-type '${advanced.plasmidfinder_type}' |
54 #end if | 58 #end if |
55 | 59 |
56 --output-summary $summary | 60 --output-summary '$summary' |
57 --output-detailed-summary $detailed_summary | 61 --output-detailed-summary '$detailed_summary' |
58 --output-resfinder $resfinder | 62 --output-resfinder '$resfinder' |
59 --output-plasmidfinder $plasmidfinder | 63 --output-plasmidfinder '$plasmidfinder' |
60 #if str($use_pointfinder) != 'disabled' | 64 --output-settings '$settings' |
61 --output-pointfinder $pointfinder | 65 --output-excel '$excel_proper_extension' |
62 #end if | 66 --output-mlst '$mlst' |
63 --output-settings $settings | |
64 --output-excel $excel_proper_extension | |
65 --output-mlst $mlst | |
66 | 67 |
67 --output-hits-dir staramr_hits | 68 --output-hits-dir staramr_hits |
68 | 69 |
69 #if str($use_pointfinder) != 'disabled' | 70 #if str($pointfinder_db.use_pointfinder) != 'disabled' |
70 --pointfinder-organism '${use_pointfinder}' | 71 --output-pointfinder '$pointfinder' |
72 #if str($pointfinder_db.use_pointfinder) == 'custom' | |
73 --pointfinder-organism '${pointfinder_db.pointfinder_custom}' | |
74 #else | |
75 --pointfinder-organism '${pointfinder_db.use_pointfinder}' | |
76 #end if | |
71 #end if | 77 #end if |
72 | 78 |
73 $named_genomes | 79 $named_genomes |
74 ]]></command> | 80 ]]></command> |
75 <inputs> | 81 <inputs> |
76 <param type="data" name="genomes" format="fasta" multiple="true"/> | 82 <param type="data" name="genomes" format="fasta" multiple="true"/> |
77 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> | 83 <conditional name="pointfinder_db"> |
78 <option value="disabled" selected="true">Disable PointFinder</option> | 84 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> |
79 <option value="salmonella">Salmonella</option> | 85 <option value="disabled" selected="true">Disable PointFinder</option> |
80 <option value="campylobacter">Campylobacter</option> | 86 <option value="salmonella">Salmonella</option> |
81 </param> | 87 <option value="campylobacter">Campylobacter</option> |
88 <option value="custom">Unvalidated</option> | |
89 </param> | |
90 <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism --> | |
91 <when value="disabled"/> | |
92 <when value="salmonella"/> | |
93 <when value="campylobacter"/> | |
94 | |
95 <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms --> | |
96 <when value="custom"> | |
97 <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results."> | |
98 <option value="enterococcus_faecalis">enterococcus_faecalis</option> | |
99 <option value="enterococcus_faecium">enterococcus_faecium</option> | |
100 <option value="escherichia_coli" selected="true">escherichia_coli</option> | |
101 <option value="helicobacter_pylori">helicobacter_pylori</option> | |
102 <option value="klebsiella">klebsiella</option> | |
103 <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option> | |
104 <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option> | |
105 <option value="plasmodium_falciparum">plasmodium_falciparum</option> | |
106 <option value="staphylococcus_aureus">staphylococcus_aureus</option> | |
107 </param> | |
108 </when> | |
109 </conditional> | |
82 <section name="advanced" title="Advanced options" expanded="false"> | 110 <section name="advanced" title="Advanced options" expanded="false"> |
83 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" | 111 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" |
84 min="0" max="100" help="(--pid-threshold)" /> | 112 min="0" max="100" help="(--pid-threshold)" /> |
85 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" | 113 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" |
86 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> | 114 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> |
101 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" | 129 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" |
102 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> | 130 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> |
103 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> | 131 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> |
104 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> | 132 <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"> | 133 <param name="mlst_scheme" type="select" label="MLST Scheme"> |
106 <option value="auto" selected="true">Automatic</option> | 134 <option value="auto" selected="true">Automatic</option> |
107 <option value="abaumannii">Acinetobacter baumannii</option> | 135 <option value="aactinomycetemcomitans">aactinomycetemcomitans</option> |
108 <option value="abaumannii_2">Acinetobacter baumannii</option> | 136 <option value="abaumannii">abaumannii</option> |
109 <option value="achromobacter">Achromobacter </option> | 137 <option value="abaumannii_2">abaumannii_2</option> |
110 <option value="aeromonas">Aeromonas </option> | 138 <option value="achromobacter">achromobacter</option> |
111 <option value="afumigatus">Aspergillus afumigatus</option> | 139 <option value="aeromonas">aeromonas</option> |
112 <option value="aphagocytophilum">Anaplasma aphagocytophilum</option> | 140 <option value="aphagocytophilum">aphagocytophilum</option> |
113 <option value="arcobacter">Arcobacter </option> | 141 <option value="arcobacter">arcobacter</option> |
114 <option value="bburgdorferi">Borrelia burgdorferi</option> | 142 <option value="bbacilliformis">bbacilliformis</option> |
115 <option value="bcc">Burkholderia cepacia</option> | 143 <option value="bcc">bcc</option> |
116 <option value="bcereus">Bacillus cereus</option> | 144 <option value="bcereus">bcereus</option> |
117 <option value="bhampsonii">Brachyspira hampsonii</option> | 145 <option value="bfragilis">bfragilis</option> |
118 <option value="bhenselae">Bartonella henselae</option> | 146 <option value="bhenselae">bhenselae</option> |
119 <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option> | 147 <option value="blicheniformis_14">blicheniformis_14</option> |
120 <option value="bifidobacterium">Bifidobacterium bifidobacterium</option> | 148 <option value="bordetella_3">bordetella_3</option> |
121 <option value="bintermedia">Brachyspira intermedia</option> | 149 <option value="borrelia">borrelia</option> |
122 <option value="blicheniformis">Bacillus licheniformis</option> | 150 <option value="bpseudomallei">bpseudomallei</option> |
123 <option value="bordetella">Bordetella pertussis</option> | 151 <option value="brachyspira">brachyspira</option> |
124 <option value="borrelia">Borrelia </option> | 152 <option value="brachyspira_2">brachyspira_2</option> |
125 <option value="bpilosicoli">Brachyspira pilosicoli</option> | 153 <option value="brachyspira_3">brachyspira_3</option> |
126 <option value="bpseudomallei">Burkholderia pseudomallei</option> | 154 <option value="brachyspira_4">brachyspira_4</option> |
127 <option value="brachyspira">Brachyspira </option> | 155 <option value="brachyspira_5">brachyspira_5</option> |
128 <option value="bsubtilis">Bacillus subtilis</option> | 156 <option value="brucella">brucella</option> |
129 <option value="calbicans">Candida albicans</option> | 157 <option value="bsubtilis">bsubtilis</option> |
130 <option value="campylobacter">Campylobacter coli</option> | 158 <option value="bwashoensis">bwashoensis</option> |
131 <option value="campylobacter">Campylobacter jejuni</option> | 159 <option value="campylobacter">campylobacter</option> |
132 <option value="cbotulinum">Clostridium botulinum</option> | 160 <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option> |
133 <option value="cconcisus">Campylobacter concisus</option> | 161 <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option> |
134 <option value="cdifficile">Clostridium difficile</option> | 162 <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option> |
135 <option value="cdifficile">Peptoclostridium difficile</option> | 163 <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option> |
136 <option value="cdifficile_2">Clostridium difficile</option> | 164 <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option> |
137 <option value="cdiphtheriae">Corynebacterium diphtheriae</option> | 165 <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option> |
138 <option value="cfetus">Campylobacter fetus</option> | 166 <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option> |
139 <option value="cfreundii">Citrobacter freundii</option> | 167 <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option> |
140 <option value="cglabrata">Candida glabrata</option> | 168 <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</option> |
141 <option value="chelveticus">Campylobacter helveticus</option> | 169 <option value="cbotulinum">cbotulinum</option> |
142 <option value="chlamydiales">Chlamydia </option> | 170 <option value="cdifficile">cdifficile</option> |
143 <option value="chyointestinalis">Campylobacter hyointestinalis</option> | 171 <option value="cfreundii">cfreundii</option> |
144 <option value="cinsulaenigrae">Campylobacter insulaenigrae</option> | 172 <option value="chlamydiales">chlamydiales</option> |
145 <option value="ckrusei">Candida krusei</option> | 173 <option value="cmaltaromaticum">cmaltaromaticum</option> |
146 <option value="clanienae">Campylobacter lanienae</option> | 174 <option value="cperfringens">cperfringens</option> |
147 <option value="clari">Campylobacter lari</option> | 175 <option value="cronobacter">cronobacter</option> |
148 <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option> | 176 <option value="csepticum">csepticum</option> |
149 <option value="cneoformans">Cryptococcus neoformans</option> | 177 <option value="diphtheria_3">diphtheria_3</option> |
150 <option value="cronobacter">Cronobacter </option> | 178 <option value="dnodosus">dnodosus</option> |
151 <option value="csepticum">Clostridium septicum</option> | 179 <option value="ecloacae">ecloacae</option> |
152 <option value="csinensis">Clonorchis sinensis</option> | 180 <option value="ecoli">ecoli</option> |
153 <option value="csputorum">Campylobacter sputorum</option> | 181 <option value="ecoli_achtman_4">ecoli_achtman_4</option> |
154 <option value="ctropicalis">Candida tropicalis</option> | 182 <option value="edwardsiella">edwardsiella</option> |
155 <option value="cupsaliensis">Campylobacter upsaliensis</option> | 183 <option value="efaecalis">efaecalis</option> |
156 <option value="ecloacae">Enterobacter cloacae</option> | 184 <option value="efaecium">efaecium</option> |
157 <option value="ecoli">Escherichia </option> | 185 <option value="fpsychrophilum">fpsychrophilum</option> |
158 <option value="ecoli">Shigella </option> | 186 <option value="gallibacterium">gallibacterium</option> |
159 <option value="ecoli_2">Escherichia </option> | 187 <option value="geotrichum">geotrichum</option> |
160 <option value="edwardsiella">Edwardsiella tarda</option> | 188 <option value="hcinaedi">hcinaedi</option> |
161 <option value="efaecalis">Enterococcus faecalis</option> | 189 <option value="helicobacter">helicobacter</option> |
162 <option value="efaecium">Enterococcus faecium</option> | 190 <option value="hinfluenzae">hinfluenzae</option> |
163 <option value="fpsychrophilum">Flavobacterium psychrophilum</option> | 191 <option value="hparasuis">hparasuis</option> |
164 <option value="haemophilus">Haemophilus </option> | 192 <option value="hsuis">hsuis</option> |
165 <option value="hcinaedi">Helicobacter cinaedi</option> | 193 <option value="kaerogenes">kaerogenes</option> |
166 <option value="hinfluenzae">Haemophilus influenzae</option> | 194 <option value="kingella">kingella</option> |
167 <option value="hparasuis">Haemophilus parasuis</option> | 195 <option value="klebsiella">klebsiella</option> |
168 <option value="hpylori">Helicobacter pylori</option> | 196 <option value="koxytoca">koxytoca</option> |
169 <option value="hsuis">Haematopinus suis</option> | 197 <option value="leptospira">leptospira</option> |
170 <option value="kkingae">Kingella kingae</option> | 198 <option value="leptospira_2">leptospira_2</option> |
171 <option value="koxytoca">Klebsiella oxytoca</option> | 199 <option value="leptospira_3">leptospira_3</option> |
172 <option value="kpneumoniae">Klebsiella pneumoniae</option> | 200 <option value="liberibacter">liberibacter</option> |
173 <option value="kseptempunctata">Kudoa septempunctata</option> | 201 <option value="listeria_2">listeria_2</option> |
174 <option value="lcasei">Lactobacillus casei</option> | 202 <option value="llactis_phage">llactis_phage</option> |
175 <option value="legionella">Legionella </option> | 203 <option value="lsalivarius">lsalivarius</option> |
176 <option value="leptospira">Leptospira </option> | 204 <option value="mabscessus">mabscessus</option> |
177 <option value="leptospira_2">Leptospira </option> | 205 <option value="magalactiae">magalactiae</option> |
178 <option value="leptospira_3">Leptospira </option> | 206 <option value="manserisalpingitidis">manserisalpingitidis</option> |
179 <option value="lmonocytogenes">Listeria monocytogenes</option> | 207 <option value="mbovis_2">mbovis_2</option> |
180 <option value="lsalivarius">Lactobacillus salivarius</option> | 208 <option value="mcanis">mcanis</option> |
181 <option value="mabscessus">Mycobacterium abscessus</option> | 209 <option value="mcaseolyticus">mcaseolyticus</option> |
182 <option value="magalactiae">Mycoplasma agalactiae</option> | 210 <option value="mcatarrhalis_achtman_6">mcatarrhalis_achtman_6</option> |
183 <option value="mbovis">Mycoplasma bovis</option> | 211 <option value="mflocculare">mflocculare</option> |
184 <option value="mcatarrhalis">Moraxells catarrhalis</option> | 212 <option value="mgallisepticum">mgallisepticum</option> |
185 <option value="mhaemolytica">Mannheimia haemolytica</option> | 213 <option value="mgallisepticum_2">mgallisepticum_2</option> |
186 <option value="mhyorhinis">Mycoplasma hyorhinis</option> | 214 <option value="mhaemolytica">mhaemolytica</option> |
187 <option value="mmassiliense">Mycobacterium massiliense</option> | 215 <option value="mhominis_3">mhominis_3</option> |
188 <option value="mplutonius">Melissococcus plutonius</option> | 216 <option value="mhyopneumoniae">mhyopneumoniae</option> |
189 <option value="neisseria">Neisseria </option> | 217 <option value="mhyorhinis">mhyorhinis</option> |
190 <option value="orhinotracheale">Ornithobacterium rhinotracheale</option> | 218 <option value="miowae">miowae</option> |
191 <option value="otsutsugamushi">Orientia tsutsugamushi</option> | 219 <option value="mplutonius">mplutonius</option> |
192 <option value="pacnes">Propionibacterium acnes</option> | 220 <option value="mpneumoniae">mpneumoniae</option> |
193 <option value="paeruginosa">Pseudomonas aeruginosa</option> | 221 <option value="msciuri">msciuri</option> |
194 <option value="pagglomerans">Pantoea agglomerans</option> | 222 <option value="msynoviae">msynoviae</option> |
195 <option value="pfluorescens">Pseudomonas fluorescens</option> | 223 <option value="mycobacteria_2">mycobacteria_2</option> |
196 <option value="pfreudenreichii">Propionibacterium freudenreichii</option> | 224 <option value="neisseria">neisseria</option> |
197 <option value="pgingivalis">Porphyromonas gingivalis</option> | 225 <option value="oralstrep">oralstrep</option> |
198 <option value="plarvae">Paenibacillus larvae</option> | 226 <option value="orhinotracheale">orhinotracheale</option> |
199 <option value="pmultocida_multihost">Pasteurella multocida</option> | 227 <option value="otsutsugamushi">otsutsugamushi</option> |
200 <option value="pmultocida_rirdc">Pasteurella multocida</option> | 228 <option value="pacnes_3">pacnes_3</option> |
201 <option value="ppentosaceus">Pediococcus pentosaceus</option> | 229 <option value="paeruginosa">paeruginosa</option> |
202 <option value="pshigelloides">Plesiomonas shigelloides</option> | 230 <option value="pdamselae">pdamselae</option> |
203 <option value="ranatipestifer">Riemerella anatipestifer</option> | 231 <option value="pfluorescens">pfluorescens</option> |
204 <option value="sagalactiae">Streptococcus agalactiae</option> | 232 <option value="pgingivalis">pgingivalis</option> |
205 <option value="saureus">Staphylococcus aureus</option> | 233 <option value="plarvae">plarvae</option> |
206 <option value="scanis">Streptococcus canis</option> | 234 <option value="pmultocida">pmultocida</option> |
207 <option value="sdysgalactiae">Streptococcus dysgalactiae</option> | 235 <option value="pmultocida_2">pmultocida_2</option> |
208 <option value="senterica">Salmonella enterica</option> | 236 <option value="ppentosaceus">ppentosaceus</option> |
209 <option value="sepidermidis">Staphylococcus epidermidis</option> | 237 <option value="pputida">pputida</option> |
210 <option value="sgallolyticus">Streptococcus gallolyticus</option> | 238 <option value="psalmonis">psalmonis</option> |
211 <option value="shaemolyticus">Staphylococcus haemolyticus</option> | 239 <option value="ranatipestifer">ranatipestifer</option> |
212 <option value="shominis">Stapylococcus hominis</option> | 240 <option value="rhodococcus">rhodococcus</option> |
213 <option value="sinorhizobium">Sinorhizobium </option> | 241 <option value="sagalactiae">sagalactiae</option> |
214 <option value="slugdunensis">Staphylococcus lugdunensis</option> | 242 <option value="saureus">saureus</option> |
215 <option value="smaltophilia">Stenotrophomonas maltophilia</option> | 243 <option value="sbsec">sbsec</option> |
216 <option value="soralis">Streptococcus oralis</option> | 244 <option value="scanis">scanis</option> |
217 <option value="spneumoniae">Streptococcus pneumoniae</option> | 245 <option value="schromogenes">schromogenes</option> |
218 <option value="spseudintermedius">Staphylococcus pseudintermedius</option> | 246 <option value="sdysgalactiae">sdysgalactiae</option> |
219 <option value="spyogenes">Streptococcus pyogenes</option> | 247 <option value="senterica_achtman_2">senterica_achtman_2</option> |
220 <option value="ssuis">Streptococcus suis</option> | 248 <option value="sepidermidis">sepidermidis</option> |
221 <option value="sthermophilus">Streptococcus thermophilus</option> | 249 <option value="sgallolyticus">sgallolyticus</option> |
222 <option value="sthermophilus_2">Streptococcus thermophilus</option> | 250 <option value="shaemolyticus">shaemolyticus</option> |
223 <option value="streptomyces">Streptomyces </option> | 251 <option value="shewanella">shewanella</option> |
224 <option value="suberis">Streptococcus uberis</option> | 252 <option value="shominis">shominis</option> |
225 <option value="szooepidemicus">Streptococcus equi</option> | 253 <option value="sinorhizobium">sinorhizobium</option> |
226 <option value="taylorella">Taylorella </option> | 254 <option value="smaltophilia">smaltophilia</option> |
227 <option value="tenacibaculum">Tenacibaculum </option> | 255 <option value="spneumoniae">spneumoniae</option> |
228 <option value="tvaginalis">Trichomonas vaginalis</option> | 256 <option value="spseudintermedius">spseudintermedius</option> |
229 <option value="vcholerae">Vibrio cholerae</option> | 257 <option value="spyogenes">spyogenes</option> |
230 <option value="vibrio">Vibrio </option> | 258 <option value="ssuis">ssuis</option> |
231 <option value="vparahaemolyticus">Vibrio parahaemolyticus</option> | 259 <option value="staphlugdunensis">staphlugdunensis</option> |
232 <option value="vtapetis">Vibrio tapetis</option> | 260 <option value="sthermophilus">sthermophilus</option> |
233 <option value="vvulnificus">Vibrio vulnificus</option> | 261 <option value="streptomyces">streptomyces</option> |
234 <option value="wolbachia">Wolbachia </option> | 262 <option value="streptothermophilus">streptothermophilus</option> |
235 <option value="xfastidiosa">Xylella fastidiosa</option> | 263 <option value="suberis">suberis</option> |
236 <option value="yersinia">Yersinia </option> | 264 <option value="szooepidemicus">szooepidemicus</option> |
237 <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option> | 265 <option value="taylorella">taylorella</option> |
238 <option value="yruckeri">Yersinia ruckeri</option> | 266 <option value="tenacibaculum">tenacibaculum</option> |
267 <option value="tpallidum">tpallidum</option> | |
268 <option value="ureaplasma">ureaplasma</option> | |
269 <option value="vcholerae">vcholerae</option> | |
270 <option value="vcholerae_2">vcholerae_2</option> | |
271 <option value="vibrio">vibrio</option> | |
272 <option value="vparahaemolyticus">vparahaemolyticus</option> | |
273 <option value="vtapetis">vtapetis</option> | |
274 <option value="vvulnificus">vvulnificus</option> | |
275 <option value="wolbachia">wolbachia</option> | |
276 <option value="xfastidiosa">xfastidiosa</option> | |
277 <option value="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option> | |
278 <option value="yruckeri">yruckeri</option> | |
239 </param> | 279 </param> |
240 <conditional name="exclude_genes"> | 280 <conditional name="exclude_genes"> |
241 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results"> | 281 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results"> |
242 <option value="default" selected="true">Exclude default list of AMR genes</option> | 282 <option value="default" selected="true">Exclude default list of AMR genes</option> |
243 <option value="custom">Provide a custom list of AMR genes to exclude</option> | 283 <option value="custom">Provide a custom list of AMR genes to exclude</option> |
261 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> | 301 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> |
262 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> | 302 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> |
263 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> | 303 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> |
264 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> | 304 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> |
265 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> | 305 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> |
266 <filter>use_pointfinder != "disabled"</filter> | 306 <filter>pointfinder_db['use_pointfinder'] != "disabled"</filter> |
267 </data> | 307 </data> |
268 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> | 308 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> |
269 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> | 309 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> |
270 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> | 310 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> |
271 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" /> | 311 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" /> |
272 </collection> | 312 </collection> |
273 </outputs> | 313 </outputs> |
274 <tests> | 314 <tests> |
275 <test> | 315 <test> |
276 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 316 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
277 <param name="use_pointfinder" value="salmonella" /> | 317 <param name="use_pointfinder" value="salmonella" /> |
278 | 318 |
279 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> | 319 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> |
280 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> | 320 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> |
281 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> | 321 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> |
282 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> | 322 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> |
283 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> | 323 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> |
284 <output_collection name="blast_hits" type="list"> | 324 <output_collection name="blast_hits" type="list"> |
285 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> | 325 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
286 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> | 326 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
287 </output_collection> | 327 </output_collection> |
288 </test> | 328 </test> |
289 <test> | 329 <test> |
290 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 330 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
331 <param name="use_pointfinder" value="custom" /> | |
332 <param name="pointfinder_custom" value="escherichia_coli" /> | |
333 | |
334 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" /> | |
335 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" /> | |
336 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> | |
337 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> | |
338 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" /> | |
339 </test> | |
340 <test> | |
341 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> | |
291 | 342 |
292 <output name="summary" file="test2-summary.tsv" ftype="tabular" /> | 343 <output name="summary" file="test2-summary.tsv" ftype="tabular" /> |
293 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" /> | 344 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" /> |
294 <output_collection name="blast_hits" type="list"> | 345 <output_collection name="blast_hits" type="list"> |
295 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> | 346 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
296 </output_collection> | 347 </output_collection> |
297 </test> | 348 </test> |
298 <test> | 349 <test> |
299 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 350 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
300 <section name="advanced"> | 351 <section name="advanced"> |
301 <param name="mlst_scheme" value="kpneumoniae" /> | 352 <param name="mlst_scheme" value="listeria_2" /> |
302 </section> | 353 </section> |
303 <output name="mlst" file="mlst.tsv" ftype="tabular" /> | 354 <output name="mlst" file="mlst.tsv" ftype="tabular" /> |
304 </test> | 355 </test> |
305 <test> | 356 <test> |
306 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> | 357 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
307 <param name="pid_threshold" value="99.8" /> | 358 <param name="pid_threshold" value="99.8" /> |
308 | 359 |
309 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> | 360 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> |
310 </test> | 361 </test> |
311 <test> | 362 <test> |
312 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" /> | 363 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" /> |
313 <param name="pid_threshold" value="99.8" /> | 364 <param name="pid_threshold" value="99.8" /> |
314 | 365 |
315 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> | 366 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> |
316 </test> | 367 </test> |
317 <test> | 368 <test> |
318 <param name="genomes" value="test-aminoglycoside.fsa" /> | 369 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
319 | 370 |
320 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> | 371 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
321 </test> | 372 </test> |
322 <test> | 373 <test> |
323 <param name="genomes" value="test-aminoglycoside.fsa" /> | 374 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
324 <param name="exclude_genes_condition" value="none" /> | 375 <param name="exclude_genes_condition" value="none" /> |
325 | 376 |
326 <output name="summary" file="test6-summary.tsv" ftype="tabular" /> | 377 <output name="summary" file="test6-summary.tsv" ftype="tabular" /> |
327 </test> | 378 </test> |
328 <test> | 379 <test> |
329 <param name="genomes" value="test-aminoglycoside.fsa" /> | 380 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
330 <param name="exclude_genes_condition" value="custom" /> | 381 <param name="exclude_genes_condition" value="custom" /> |
331 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> | 382 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> |
332 | 383 |
333 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> | 384 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
334 </test> | 385 </test> |
335 <test> | 386 <test> |
336 <param name="genomes" value="test-aminoglycoside.fsa" /> | 387 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
337 <param name="genome_size_lower_bound" value="1" /> | 388 <param name="genome_size_lower_bound" value="1" /> |
338 <param name="genome_size_upper_bound" value="10" /> | 389 <param name="genome_size_upper_bound" value="10" /> |
339 | 390 |
340 <output name="summary" file="test8-summary.tsv" ftype="tabular"/> | 391 <output name="summary" file="test8-summary.tsv" ftype="tabular"/> |
341 </test> | 392 </test> |
555 | 606 |
556 .. _staramr: https://github.com/phac-nml/staramr | 607 .. _staramr: https://github.com/phac-nml/staramr |
557 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db | 608 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db |
558 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db | 609 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db |
559 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db | 610 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db |
560 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/ | 611 .. _webservice: https://cge.food.dtu.dk/services/ResFinder/ |
561 ]]></help> | 612 ]]></help> |
562 <citations> | 613 <citations> |
563 <citation type="bibtex"> | 614 <citation type="bibtex"> |
564 @misc{githubstaramr, | 615 @Article{microorganisms10020292, |
565 author = {Petkau, Aaron}, | 616 AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.}, |
566 year = {2018}, | 617 TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr}, |
567 title = {staramr}, | 618 JOURNAL = {Microorganisms}, |
568 publisher = {GitHub}, | 619 VOLUME = {10}, |
569 journal = {GitHub repository}, | 620 YEAR = {2022}, |
570 url = {https://github.com/phac-nml/staramr}, | 621 NUMBER = {2}, |
571 }</citation> | 622 ARTICLE-NUMBER = {292}, |
623 URL = {https://www.mdpi.com/2076-2607/10/2/292}, | |
624 ISSN = {2076-2607}, | |
625 DOI = {10.3390/microorganisms10020292} | |
626 } | |
627 </citation> | |
572 </citations> | 628 </citations> |
573 </tool> | 629 </tool> |