Mercurial > repos > iuc > mlst
comparison mlst.xml @ 4:1f5641a52664 draft
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 |
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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)" /> |