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comparison mlst.xml @ 4:1f5641a52664 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe
author iuc
date Sat, 29 Dec 2018 13:30:32 -0500
parents 68cdb40ff91c
children 31812e7a1315
comparison
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3:68cdb40ff91c 4:1f5641a52664
61 <option value="advanced">Yes, see full parameter list.</option> 61 <option value="advanced">Yes, see full parameter list.</option>
62 </param> 62 </param>
63 <when value="simple"> 63 <when value="simple">
64 </when> 64 </when>
65 <when value="advanced"> 65 <when value="advanced">
66 <param argument="--minid" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" /> 66 <param argument="--minid" type="integer" label="Minimum DNA %identity" value="95" min="0" max="100" help="Minimum DNA %identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
67 <param argument="--mincov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" /> 67 <param argument="--mincov" type="integer" label="Minimum DNA %coverage" value="10" help="Minimum DNA %coverage to report partial allele at all (default 10, must be between 0-100)" optional="true" />
68 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" /> 68 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
69 <conditional name="scheme_condition"> 69 <conditional name="scheme_condition">
70 <param name="set_scheme" type="select" label="Automatically set MLST scheme"> 70 <param name="set_scheme" type="select" label="Automatically set MLST scheme">
71 <option value="auto" selected="true">Automatic MLST scheme detection</option> 71 <option value="auto" selected="true">Automatic MLST scheme detection</option>
72 <option value="list">Select from a list of MLST schemes</option> 72 <option value="list">Select from a list of MLST schemes</option>
76 <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" /> 76 <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
77 <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" /> 77 <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" />
78 </when> 78 </when>
79 <when value="list"> 79 <when value="list">
80 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme"> 80 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
81 <option value="abaumannii">abaumannii</option>
82 <option value="abaumannii_2">abaumannii_2</option>
81 <option value="achromobacter">achromobacter</option> 83 <option value="achromobacter">achromobacter</option>
82 <option value="vvulnificus">vvulnificus</option> 84 <option value="aeromonas">aeromonas</option>
83 <option value="cglabrata">cglabrata</option> 85 <option value="aphagocytophilum">aphagocytophilum</option>
84 <option value="sthermophilus_2">sthermophilus_2</option> 86 <option value="arcobacter">arcobacter</option>
87 <option value="bbacilliformis">bbacilliformis</option>
88 <option value="bcc">bcc</option>
89 <option value="bcereus">bcereus</option>
90 <option value="bhampsonii">bhampsonii</option>
91 <option value="bhenselae">bhenselae</option>
92 <option value="bhyodysenteriae">bhyodysenteriae</option>
93 <option value="bintermedia">bintermedia</option>
94 <option value="blicheniformis">blicheniformis</option>
95 <option value="bordetella">bordetella</option>
96 <option value="borrelia">borrelia</option>
97 <option value="bpilosicoli">bpilosicoli</option>
98 <option value="bpseudomallei">bpseudomallei</option>
99 <option value="brachyspira">brachyspira</option>
100 <option value="brucella">brucella</option>
101 <option value="bsubtilis">bsubtilis</option>
102 <option value="campylobacter">campylobacter</option>
103 <option value="cbotulinum">cbotulinum</option>
104 <option value="cconcisus">cconcisus</option>
105 <option value="cdifficile">cdifficile</option>
106 <option value="cdiphtheriae">cdiphtheriae</option>
107 <option value="cfetus">cfetus</option>
108 <option value="cfreundii">cfreundii</option>
109 <option value="chelveticus">chelveticus</option>
110 <option value="chlamydiales">chlamydiales</option>
111 <option value="chyointestinalis">chyointestinalis</option>
112 <option value="cinsulaenigrae">cinsulaenigrae</option>
113 <option value="clanienae">clanienae</option>
114 <option value="clari">clari</option>
115 <option value="cmaltaromaticum">cmaltaromaticum</option>
116 <option value="cronobacter">cronobacter</option>
117 <option value="csepticum">csepticum</option>
118 <option value="csputorum">csputorum</option>
119 <option value="cupsaliensis">cupsaliensis</option>
120 <option value="dnodosus">dnodosus</option>
121 <option value="ecloacae">ecloacae</option>
122 <option value="ecoli">ecoli</option>
123 <option value="ecoli_2">ecoli_2</option>
124 <option value="edwardsiella">edwardsiella</option>
125 <option value="efaecalis">efaecalis</option>
126 <option value="efaecium">efaecium</option>
127 <option value="fpsychrophilum">fpsychrophilum</option>
128 <option value="ganatis">ganatis</option>
129 <option value="hcinaedi">hcinaedi</option>
130 <option value="hinfluenzae">hinfluenzae</option>
131 <option value="hparasuis">hparasuis</option>
132 <option value="hpylori">hpylori</option>
133 <option value="hsuis">hsuis</option>
134 <option value="kaerogenes">kaerogenes</option>
135 <option value="kkingae">kkingae</option>
136 <option value="koxytoca">koxytoca</option>
137 <option value="kpneumoniae">kpneumoniae</option>
138 <option value="leptospira">leptospira</option>
139 <option value="leptospira_2">leptospira_2</option>
140 <option value="leptospira_3">leptospira_3</option>
141 <option value="lmonocytogenes">lmonocytogenes</option>
142 <option value="lsalivarius">lsalivarius</option>
143 <option value="mabscessus">mabscessus</option>
144 <option value="magalactiae">magalactiae</option>
145 <option value="mbovis">mbovis</option>
146 <option value="mcanis">mcanis</option>
147 <option value="mcaseolyticus">mcaseolyticus</option>
148 <option value="mcatarrhalis">mcatarrhalis</option>
149 <option value="mhaemolytica">mhaemolytica</option>
150 <option value="mhyopneumoniae">mhyopneumoniae</option>
151 <option value="mhyorhinis">mhyorhinis</option>
152 <option value="miowae">miowae</option>
85 <option value="mmassiliense">mmassiliense</option> 153 <option value="mmassiliense">mmassiliense</option>
86 <option value="bhampsonii">bhampsonii</option> 154 <option value="mplutonius">mplutonius</option>
87 <option value="afumigatus">afumigatus</option> 155 <option value="mpneumoniae">mpneumoniae</option>
88 <option value="ecloacae">ecloacae</option> 156 <option value="msynoviae">msynoviae</option>
89 <option value="brucella">brucella</option> 157 <option value="mycobacteria">mycobacteria</option>
90 <option value="spseudintermedius">spseudintermedius</option>
91 <option value="kpneumoniae">kpneumoniae</option>
92 <option value="edwardsiella">edwardsiella</option>
93 <option value="chlamydiales">chlamydiales</option>
94 <option value="leptospira_2">leptospira_2</option>
95 <option value="neisseria">neisseria</option> 158 <option value="neisseria">neisseria</option>
96 <option value="vcholerae">vcholerae</option>
97 <option value="orhinotracheale">orhinotracheale</option> 159 <option value="orhinotracheale">orhinotracheale</option>
160 <option value="otsutsugamushi">otsutsugamushi</option>
161 <option value="pacnes">pacnes</option>
98 <option value="paeruginosa">paeruginosa</option> 162 <option value="paeruginosa">paeruginosa</option>
99 <option value="lsalivarius">lsalivarius</option> 163 <option value="pdamselae">pdamselae</option>
100 <option value="leptospira">leptospira</option> 164 <option value="pfluorescens">pfluorescens</option>
101 <option value="sepidermidis">sepidermidis</option> 165 <option value="pgingivalis">pgingivalis</option>
102 <option value="mhyorhinis">mhyorhinis</option> 166 <option value="plarvae">plarvae</option>
103 <option value="bcc">bcc</option> 167 <option value="pmultocida_multihost">pmultocida_multihost</option>
104 <option value="yruckeri">yruckeri</option> 168 <option value="pmultocida_rirdc">pmultocida_rirdc</option>
105 <option value="suberis">suberis</option> 169 <option value="ppentosaceus">ppentosaceus</option>
106 <option value="yersinia">yersinia</option> 170 <option value="pputida">pputida</option>
107 <option value="taylorella">taylorella</option> 171 <option value="psalmonis">psalmonis</option>
108 <option value="kaerogenes">kaerogenes</option>
109 <option value="xfastidiosa">xfastidiosa</option>
110 <option value="bordetella">bordetella</option>
111 <option value="cbotulinum">cbotulinum</option>
112 <option value="hpylori">hpylori</option>
113 <option value="mpneumoniae">mpneumoniae</option>
114 <option value="sdysgalactiae">sdysgalactiae</option>
115 <option value="efaecium">efaecium</option>
116 <option value="aphagocytophilum">aphagocytophilum</option>
117 <option value="ecoli_2">ecoli_2</option>
118 <option value="ganatis">ganatis</option>
119 <option value="mhyopneumoniae">mhyopneumoniae</option>
120 <option value="bsubtilis">bsubtilis</option>
121 <option value="tenacibaculum">tenacibaculum</option>
122 <option value="campylobacter">campylobacter</option>
123 <option value="ranatipestifer">ranatipestifer</option> 172 <option value="ranatipestifer">ranatipestifer</option>
124 <option value="mcaseolyticus">mcaseolyticus</option> 173 <option value="rhodococcus">rhodococcus</option>
125 <option value="csputorum">csputorum</option> 174 <option value="sagalactiae">sagalactiae</option>
126 <option value="csinensis">csinensis</option>
127 <option value="dnodosus">dnodosus</option>
128 <option value="koxytoca">koxytoca</option>
129 <option value="soralis">soralis</option>
130 <option value="bcereus">bcereus</option>
131 <option value="wolbachia">wolbachia</option>
132 <option value="saureus">saureus</option> 175 <option value="saureus">saureus</option>
133 <option value="hcinaedi">hcinaedi</option>
134 <option value="clari">clari</option>
135 <option value="leptospira_3">leptospira_3</option>
136 <option value="sinorhizobium">sinorhizobium</option>
137 <option value="pmultocida_multihost">pmultocida_multihost</option>
138 <option value="ecoli">ecoli</option>
139 <option value="pdamselae">pdamselae</option>
140 <option value="pmultocida_rirdc">pmultocida_rirdc</option>
141 <option value="bhyodysenteriae">bhyodysenteriae</option>
142 <option value="cupsaliensis">cupsaliensis</option>
143 <option value="efaecalis">efaecalis</option>
144 <option value="shaemolyticus">shaemolyticus</option>
145 <option value="rhodococcus">rhodococcus</option>
146 <option value="pacnes">pacnes</option>
147 <option value="szooepidemicus">szooepidemicus</option>
148 <option value="pgingivalis">pgingivalis</option>
149 <option value="cfetus">cfetus</option>
150 <option value="bpilosicoli">bpilosicoli</option>
151 <option value="kseptempunctata">kseptempunctata</option>
152 <option value="streptomyces">streptomyces</option>
153 <option value="smaltophilia">smaltophilia</option>
154 <option value="ppentosaceus">ppentosaceus</option>
155 <option value="cronobacter">cronobacter</option>
156 <option value="mhaemolytica">mhaemolytica</option>
157 <option value="cdiphtheriae">cdiphtheriae</option>
158 <option value="vcholerae2">vcholerae2</option>
159 <option value="chyointestinalis">chyointestinalis</option>
160 <option value="borrelia">borrelia</option>
161 <option value="abaumannii">abaumannii</option>
162 <option value="arcobacter">arcobacter</option>
163 <option value="csepticum">csepticum</option>
164 <option value="mcanis">mcanis</option>
165 <option value="pfluorescens">pfluorescens</option>
166 <option value="lmonocytogenes">lmonocytogenes</option>
167 <option value="sgallolyticus">sgallolyticus</option>
168 <option value="cfreundii">cfreundii</option>
169 <option value="mplutonius">mplutonius</option>
170 <option value="vibrio">vibrio</option>
171 <option value="bbacilliformis">bbacilliformis</option>
172 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
173 <option value="vparahaemolyticus">vparahaemolyticus</option>
174 <option value="mcatarrhalis">mcatarrhalis</option>
175 <option value="bintermedia">bintermedia</option>
176 <option value="sagalactiae">sagalactiae</option>
177 <option value="kkingae">kkingae</option>
178 <option value="bpseudomallei">bpseudomallei</option>
179 <option value="bhenselae">bhenselae</option>
180 <option value="spneumoniae">spneumoniae</option>
181 <option value="vtapetis">vtapetis</option>
182 <option value="senterica">senterica</option>
183 <option value="mabscessus">mabscessus</option>
184 <option value="sthermophilus">sthermophilus</option>
185 <option value="brachyspira">brachyspira</option>
186 <option value="mbovis">mbovis</option>
187 <option value="hsuis">hsuis</option>
188 <option value="spyogenes">spyogenes</option>
189 <option value="cconcisus">cconcisus</option>
190 <option value="cmaltaromaticum">cmaltaromaticum</option>
191 <option value="abaumannii_2">abaumannii_2</option>
192 <option value="aeromonas">aeromonas</option>
193 <option value="miowae">miowae</option>
194 <option value="shominis">shominis</option>
195 <option value="otsutsugamushi">otsutsugamushi</option>
196 <option value="hinfluenzae">hinfluenzae</option>
197 <option value="clanienae">clanienae</option>
198 <option value="sbsec">sbsec</option> 176 <option value="sbsec">sbsec</option>
199 <option value="scanis">scanis</option> 177 <option value="scanis">scanis</option>
200 <option value="msynoviae">msynoviae</option> 178 <option value="sdysgalactiae">sdysgalactiae</option>
201 <option value="hparasuis">hparasuis</option> 179 <option value="senterica">senterica</option>
202 <option value="magalactiae">magalactiae</option> 180 <option value="sepidermidis">sepidermidis</option>
203 <option value="chelveticus">chelveticus</option> 181 <option value="sgallolyticus">sgallolyticus</option>
204 <option value="fpsychrophilum">fpsychrophilum</option> 182 <option value="shaemolyticus">shaemolyticus</option>
183 <option value="shominis">shominis</option>
184 <option value="sinorhizobium">sinorhizobium</option>
185 <option value="slugdunensis">slugdunensis</option>
186 <option value="smaltophilia">smaltophilia</option>
187 <option value="soralis">soralis</option>
188 <option value="spneumoniae">spneumoniae</option>
189 <option value="spseudintermedius">spseudintermedius</option>
190 <option value="spyogenes">spyogenes</option>
205 <option value="ssuis">ssuis</option> 191 <option value="ssuis">ssuis</option>
206 <option value="cdifficile">cdifficile</option> 192 <option value="sthermophilus">sthermophilus</option>
207 <option value="cinsulaenigrae">cinsulaenigrae</option> 193 <option value="sthermophilus_2">sthermophilus_2</option>
208 <option value="blicheniformis">blicheniformis</option> 194 <option value="streptomyces">streptomyces</option>
209 <option value="slugdunensis">slugdunensis</option> 195 <option value="suberis">suberis</option>
210 <option value="plarvae">plarvae</option> 196 <option value="szooepidemicus">szooepidemicus</option>
197 <option value="taylorella">taylorella</option>
198 <option value="tenacibaculum">tenacibaculum</option>
199 <option value="tpallidum">tpallidum</option>
200 <option value="ureaplasma">ureaplasma</option>
201 <option value="vcholerae">vcholerae</option>
202 <option value="vcholerae2">vcholerae2</option>
203 <option value="vibrio">vibrio</option>
204 <option value="vparahaemolyticus">vparahaemolyticus</option>
205 <option value="vtapetis">vtapetis</option>
206 <option value="vvulnificus">vvulnificus</option>
207 <option value="wolbachia">wolbachia</option>
208 <option value="xfastidiosa">xfastidiosa</option>
209 <option value="yersinia">yersinia</option>
210 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
211 <option value="yruckeri">yruckeri</option>
211 </param> 212 </param>
212 <expand macro="legacy_param" /> 213 <expand macro="legacy_param" />
213 </when> 214 </when>
214 <when value="manual"> 215 <when value="manual">
215 <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" /> 216 <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" />