Mercurial > repos > iuc > mlst
diff 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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--- a/mlst.xml Mon Oct 15 07:41:48 2018 -0400 +++ b/mlst.xml Sat Dec 29 13:30:32 2018 -0500 @@ -63,8 +63,8 @@ <when value="simple"> </when> <when value="advanced"> - <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" /> - <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" /> + <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" /> + <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" /> <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" /> <conditional name="scheme_condition"> <param name="set_scheme" type="select" label="Automatically set MLST scheme"> @@ -78,136 +78,137 @@ </when> <when value="list"> <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme"> + <option value="abaumannii">abaumannii</option> + <option value="abaumannii_2">abaumannii_2</option> <option value="achromobacter">achromobacter</option> - <option value="vvulnificus">vvulnificus</option> - <option value="cglabrata">cglabrata</option> - <option value="sthermophilus_2">sthermophilus_2</option> - <option value="mmassiliense">mmassiliense</option> + <option value="aeromonas">aeromonas</option> + <option value="aphagocytophilum">aphagocytophilum</option> + <option value="arcobacter">arcobacter</option> + <option value="bbacilliformis">bbacilliformis</option> + <option value="bcc">bcc</option> + <option value="bcereus">bcereus</option> <option value="bhampsonii">bhampsonii</option> - <option value="afumigatus">afumigatus</option> - <option value="ecloacae">ecloacae</option> + <option value="bhenselae">bhenselae</option> + <option value="bhyodysenteriae">bhyodysenteriae</option> + <option value="bintermedia">bintermedia</option> + <option value="blicheniformis">blicheniformis</option> + <option value="bordetella">bordetella</option> + <option value="borrelia">borrelia</option> + <option value="bpilosicoli">bpilosicoli</option> + <option value="bpseudomallei">bpseudomallei</option> + <option value="brachyspira">brachyspira</option> <option value="brucella">brucella</option> - <option value="spseudintermedius">spseudintermedius</option> - <option value="kpneumoniae">kpneumoniae</option> - <option value="edwardsiella">edwardsiella</option> + <option value="bsubtilis">bsubtilis</option> + <option value="campylobacter">campylobacter</option> + <option value="cbotulinum">cbotulinum</option> + <option value="cconcisus">cconcisus</option> + <option value="cdifficile">cdifficile</option> + <option value="cdiphtheriae">cdiphtheriae</option> + <option value="cfetus">cfetus</option> + <option value="cfreundii">cfreundii</option> + <option value="chelveticus">chelveticus</option> <option value="chlamydiales">chlamydiales</option> - <option value="leptospira_2">leptospira_2</option> - <option value="neisseria">neisseria</option> - <option value="vcholerae">vcholerae</option> - <option value="orhinotracheale">orhinotracheale</option> - <option value="paeruginosa">paeruginosa</option> - <option value="lsalivarius">lsalivarius</option> - <option value="leptospira">leptospira</option> - <option value="sepidermidis">sepidermidis</option> - <option value="mhyorhinis">mhyorhinis</option> - <option value="bcc">bcc</option> - <option value="yruckeri">yruckeri</option> - <option value="suberis">suberis</option> - <option value="yersinia">yersinia</option> - <option value="taylorella">taylorella</option> + <option value="chyointestinalis">chyointestinalis</option> + <option value="cinsulaenigrae">cinsulaenigrae</option> + <option value="clanienae">clanienae</option> + <option value="clari">clari</option> + <option value="cmaltaromaticum">cmaltaromaticum</option> + <option value="cronobacter">cronobacter</option> + <option value="csepticum">csepticum</option> + <option value="csputorum">csputorum</option> + <option value="cupsaliensis">cupsaliensis</option> + <option value="dnodosus">dnodosus</option> + <option value="ecloacae">ecloacae</option> + <option value="ecoli">ecoli</option> + <option value="ecoli_2">ecoli_2</option> + <option value="edwardsiella">edwardsiella</option> + <option value="efaecalis">efaecalis</option> + <option value="efaecium">efaecium</option> + <option value="fpsychrophilum">fpsychrophilum</option> + <option value="ganatis">ganatis</option> + <option value="hcinaedi">hcinaedi</option> + <option value="hinfluenzae">hinfluenzae</option> + <option value="hparasuis">hparasuis</option> + <option value="hpylori">hpylori</option> + <option value="hsuis">hsuis</option> <option value="kaerogenes">kaerogenes</option> - <option value="xfastidiosa">xfastidiosa</option> - <option value="bordetella">bordetella</option> - <option value="cbotulinum">cbotulinum</option> - <option value="hpylori">hpylori</option> - <option value="mpneumoniae">mpneumoniae</option> - <option value="sdysgalactiae">sdysgalactiae</option> - <option value="efaecium">efaecium</option> - <option value="aphagocytophilum">aphagocytophilum</option> - <option value="ecoli_2">ecoli_2</option> - <option value="ganatis">ganatis</option> + <option value="kkingae">kkingae</option> + <option value="koxytoca">koxytoca</option> + <option value="kpneumoniae">kpneumoniae</option> + <option value="leptospira">leptospira</option> + <option value="leptospira_2">leptospira_2</option> + <option value="leptospira_3">leptospira_3</option> + <option value="lmonocytogenes">lmonocytogenes</option> + <option value="lsalivarius">lsalivarius</option> + <option value="mabscessus">mabscessus</option> + <option value="magalactiae">magalactiae</option> + <option value="mbovis">mbovis</option> + <option value="mcanis">mcanis</option> + <option value="mcaseolyticus">mcaseolyticus</option> + <option value="mcatarrhalis">mcatarrhalis</option> + <option value="mhaemolytica">mhaemolytica</option> <option value="mhyopneumoniae">mhyopneumoniae</option> - <option value="bsubtilis">bsubtilis</option> - <option value="tenacibaculum">tenacibaculum</option> - <option value="campylobacter">campylobacter</option> - <option value="ranatipestifer">ranatipestifer</option> - <option value="mcaseolyticus">mcaseolyticus</option> - <option value="csputorum">csputorum</option> - <option value="csinensis">csinensis</option> - <option value="dnodosus">dnodosus</option> - <option value="koxytoca">koxytoca</option> - <option value="soralis">soralis</option> - <option value="bcereus">bcereus</option> - <option value="wolbachia">wolbachia</option> - <option value="saureus">saureus</option> - <option value="hcinaedi">hcinaedi</option> - <option value="clari">clari</option> - <option value="leptospira_3">leptospira_3</option> - <option value="sinorhizobium">sinorhizobium</option> - <option value="pmultocida_multihost">pmultocida_multihost</option> - <option value="ecoli">ecoli</option> + <option value="mhyorhinis">mhyorhinis</option> + <option value="miowae">miowae</option> + <option value="mmassiliense">mmassiliense</option> + <option value="mplutonius">mplutonius</option> + <option value="mpneumoniae">mpneumoniae</option> + <option value="msynoviae">msynoviae</option> + <option value="mycobacteria">mycobacteria</option> + <option value="neisseria">neisseria</option> + <option value="orhinotracheale">orhinotracheale</option> + <option value="otsutsugamushi">otsutsugamushi</option> + <option value="pacnes">pacnes</option> + <option value="paeruginosa">paeruginosa</option> <option value="pdamselae">pdamselae</option> + <option value="pfluorescens">pfluorescens</option> + <option value="pgingivalis">pgingivalis</option> + <option value="plarvae">plarvae</option> + <option value="pmultocida_multihost">pmultocida_multihost</option> <option value="pmultocida_rirdc">pmultocida_rirdc</option> - <option value="bhyodysenteriae">bhyodysenteriae</option> - <option value="cupsaliensis">cupsaliensis</option> - <option value="efaecalis">efaecalis</option> - <option value="shaemolyticus">shaemolyticus</option> - <option value="rhodococcus">rhodococcus</option> - <option value="pacnes">pacnes</option> - <option value="szooepidemicus">szooepidemicus</option> - <option value="pgingivalis">pgingivalis</option> - <option value="cfetus">cfetus</option> - <option value="bpilosicoli">bpilosicoli</option> - <option value="kseptempunctata">kseptempunctata</option> - <option value="streptomyces">streptomyces</option> - <option value="smaltophilia">smaltophilia</option> <option value="ppentosaceus">ppentosaceus</option> - <option value="cronobacter">cronobacter</option> - <option value="mhaemolytica">mhaemolytica</option> - <option value="cdiphtheriae">cdiphtheriae</option> - <option value="vcholerae2">vcholerae2</option> - <option value="chyointestinalis">chyointestinalis</option> - <option value="borrelia">borrelia</option> - <option value="abaumannii">abaumannii</option> - <option value="arcobacter">arcobacter</option> - <option value="csepticum">csepticum</option> - <option value="mcanis">mcanis</option> - <option value="pfluorescens">pfluorescens</option> - <option value="lmonocytogenes">lmonocytogenes</option> - <option value="sgallolyticus">sgallolyticus</option> - <option value="cfreundii">cfreundii</option> - <option value="mplutonius">mplutonius</option> - <option value="vibrio">vibrio</option> - <option value="bbacilliformis">bbacilliformis</option> - <option value="ypseudotuberculosis">ypseudotuberculosis</option> - <option value="vparahaemolyticus">vparahaemolyticus</option> - <option value="mcatarrhalis">mcatarrhalis</option> - <option value="bintermedia">bintermedia</option> + <option value="pputida">pputida</option> + <option value="psalmonis">psalmonis</option> + <option value="ranatipestifer">ranatipestifer</option> + <option value="rhodococcus">rhodococcus</option> <option value="sagalactiae">sagalactiae</option> - <option value="kkingae">kkingae</option> - <option value="bpseudomallei">bpseudomallei</option> - <option value="bhenselae">bhenselae</option> - <option value="spneumoniae">spneumoniae</option> - <option value="vtapetis">vtapetis</option> - <option value="senterica">senterica</option> - <option value="mabscessus">mabscessus</option> - <option value="sthermophilus">sthermophilus</option> - <option value="brachyspira">brachyspira</option> - <option value="mbovis">mbovis</option> - <option value="hsuis">hsuis</option> - <option value="spyogenes">spyogenes</option> - <option value="cconcisus">cconcisus</option> - <option value="cmaltaromaticum">cmaltaromaticum</option> - <option value="abaumannii_2">abaumannii_2</option> - <option value="aeromonas">aeromonas</option> - <option value="miowae">miowae</option> - <option value="shominis">shominis</option> - <option value="otsutsugamushi">otsutsugamushi</option> - <option value="hinfluenzae">hinfluenzae</option> - <option value="clanienae">clanienae</option> + <option value="saureus">saureus</option> <option value="sbsec">sbsec</option> <option value="scanis">scanis</option> - <option value="msynoviae">msynoviae</option> - <option value="hparasuis">hparasuis</option> - <option value="magalactiae">magalactiae</option> - <option value="chelveticus">chelveticus</option> - <option value="fpsychrophilum">fpsychrophilum</option> + <option value="sdysgalactiae">sdysgalactiae</option> + <option value="senterica">senterica</option> + <option value="sepidermidis">sepidermidis</option> + <option value="sgallolyticus">sgallolyticus</option> + <option value="shaemolyticus">shaemolyticus</option> + <option value="shominis">shominis</option> + <option value="sinorhizobium">sinorhizobium</option> + <option value="slugdunensis">slugdunensis</option> + <option value="smaltophilia">smaltophilia</option> + <option value="soralis">soralis</option> + <option value="spneumoniae">spneumoniae</option> + <option value="spseudintermedius">spseudintermedius</option> + <option value="spyogenes">spyogenes</option> <option value="ssuis">ssuis</option> - <option value="cdifficile">cdifficile</option> - <option value="cinsulaenigrae">cinsulaenigrae</option> - <option value="blicheniformis">blicheniformis</option> - <option value="slugdunensis">slugdunensis</option> - <option value="plarvae">plarvae</option> + <option value="sthermophilus">sthermophilus</option> + <option value="sthermophilus_2">sthermophilus_2</option> + <option value="streptomyces">streptomyces</option> + <option value="suberis">suberis</option> + <option value="szooepidemicus">szooepidemicus</option> + <option value="taylorella">taylorella</option> + <option value="tenacibaculum">tenacibaculum</option> + <option value="tpallidum">tpallidum</option> + <option value="ureaplasma">ureaplasma</option> + <option value="vcholerae">vcholerae</option> + <option value="vcholerae2">vcholerae2</option> + <option value="vibrio">vibrio</option> + <option value="vparahaemolyticus">vparahaemolyticus</option> + <option value="vtapetis">vtapetis</option> + <option value="vvulnificus">vvulnificus</option> + <option value="wolbachia">wolbachia</option> + <option value="xfastidiosa">xfastidiosa</option> + <option value="yersinia">yersinia</option> + <option value="ypseudotuberculosis">ypseudotuberculosis</option> + <option value="yruckeri">yruckeri</option> </param> <expand macro="legacy_param" /> </when>