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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 19f25d46a82936f0b1a7b53ca1f70d5d6ef69cbe |
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modified:
macros.xml mlst.xml |
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| diff -r 68cdb40ff91c -r 1f5641a52664 macros.xml --- a/macros.xml Mon Oct 15 07:41:48 2018 -0400 +++ b/macros.xml Sat Dec 29 13:30:32 2018 -0500 |
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| @@ -1,9 +1,9 @@ <macros> - <token name="@VERSION@">2.15.1</token> + <token name="@VERSION@">2.16.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.15.1">mlst</requirement> + <requirement type="package" version="2.16.1">mlst</requirement> </requirements> </xml> |
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| diff -r 68cdb40ff91c -r 1f5641a52664 mlst.xml --- a/mlst.xml Mon Oct 15 07:41:48 2018 -0400 +++ b/mlst.xml Sat Dec 29 13:30:32 2018 -0500 |
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| b'@@ -63,8 +63,8 @@\n <when value="simple">\n </when>\n <when value="advanced">\n- <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" />\n- <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" />\n+ <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" />\n+ <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" />\n <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />\n <conditional name="scheme_condition">\n <param name="set_scheme" type="select" label="Automatically set MLST scheme">\n@@ -78,136 +78,137 @@\n </when>\n <when value="list">\n <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">\n+ <option value="abaumannii">abaumannii</option>\n+ <option value="abaumannii_2">abaumannii_2</option>\n <option value="achromobacter">achromobacter</option>\n- <option value="vvulnificus">vvulnificus</option>\n- <option value="cglabrata">cglabrata</option>\n- <option value="sthermophilus_2">sthermophilus_2</option>\n- <option value="mmassiliense">mmassiliense</option>\n+ <option value="aeromonas">aeromonas</option>\n+ <option value="aphagocytophilum">aphagocytophilum</option>\n+ <option value="arcobacter">arcobacter</option>\n+ <option value="bbacilliformis">bbacilliformis</option>\n+ <option value="bcc">bcc</option>\n+ <option value="bcereus">bcereus</option>\n <option value="bhampsonii">bhampsonii</option>\n- <option value="afumigatus">afumigatus</option>\n- <option value="ecloacae">ecloacae</option>\n+ <option value="bhenselae">bhenselae</option>\n+ <option value="bhyodysenteriae">bhyodysenteriae</option>\n+ <option value="bintermedia">bintermedia</option>\n+ <option value="blicheniformis">blicheniformis</option>\n+ <option value="bordetella">bordetella</option>\n+ <option value="borrelia">borrelia</option>\n+ <option value="bpilosicoli">bpilosicoli</option>\n+ <option value="bpseudomallei">bpseudomallei</option>\n+ <option value="brachyspira">brachyspira</option>\n <option value="brucella">brucella</option>\n- <option value="spseudintermedius">spseudintermedius</option>\n- <option value="kpneumoniae">kpneumoniae</option>\n- <option value="edwardsiella">edwardsiella</option>\n+ <option value="bsubtilis">bsubtilis</option>\n+ <option value="campylobacter">campylobacter</option>\n+ <option value="cbotulinum">cbotulinum</option>\n+ <opti'..b'ption>\n- <option value="otsutsugamushi">otsutsugamushi</option>\n- <option value="hinfluenzae">hinfluenzae</option>\n- <option value="clanienae">clanienae</option>\n+ <option value="saureus">saureus</option>\n <option value="sbsec">sbsec</option>\n <option value="scanis">scanis</option>\n- <option value="msynoviae">msynoviae</option>\n- <option value="hparasuis">hparasuis</option>\n- <option value="magalactiae">magalactiae</option>\n- <option value="chelveticus">chelveticus</option>\n- <option value="fpsychrophilum">fpsychrophilum</option>\n+ <option value="sdysgalactiae">sdysgalactiae</option>\n+ <option value="senterica">senterica</option>\n+ <option value="sepidermidis">sepidermidis</option>\n+ <option value="sgallolyticus">sgallolyticus</option>\n+ <option value="shaemolyticus">shaemolyticus</option>\n+ <option value="shominis">shominis</option>\n+ <option value="sinorhizobium">sinorhizobium</option>\n+ <option value="slugdunensis">slugdunensis</option>\n+ <option value="smaltophilia">smaltophilia</option>\n+ <option value="soralis">soralis</option>\n+ <option value="spneumoniae">spneumoniae</option>\n+ <option value="spseudintermedius">spseudintermedius</option>\n+ <option value="spyogenes">spyogenes</option>\n <option value="ssuis">ssuis</option>\n- <option value="cdifficile">cdifficile</option>\n- <option value="cinsulaenigrae">cinsulaenigrae</option>\n- <option value="blicheniformis">blicheniformis</option>\n- <option value="slugdunensis">slugdunensis</option>\n- <option value="plarvae">plarvae</option>\n+ <option value="sthermophilus">sthermophilus</option>\n+ <option value="sthermophilus_2">sthermophilus_2</option>\n+ <option value="streptomyces">streptomyces</option>\n+ <option value="suberis">suberis</option>\n+ <option value="szooepidemicus">szooepidemicus</option>\n+ <option value="taylorella">taylorella</option>\n+ <option value="tenacibaculum">tenacibaculum</option>\n+ <option value="tpallidum">tpallidum</option>\n+ <option value="ureaplasma">ureaplasma</option>\n+ <option value="vcholerae">vcholerae</option>\n+ <option value="vcholerae2">vcholerae2</option>\n+ <option value="vibrio">vibrio</option>\n+ <option value="vparahaemolyticus">vparahaemolyticus</option>\n+ <option value="vtapetis">vtapetis</option>\n+ <option value="vvulnificus">vvulnificus</option>\n+ <option value="wolbachia">wolbachia</option>\n+ <option value="xfastidiosa">xfastidiosa</option>\n+ <option value="yersinia">yersinia</option>\n+ <option value="ypseudotuberculosis">ypseudotuberculosis</option>\n+ <option value="yruckeri">yruckeri</option>\n </param>\n <expand macro="legacy_param" />\n </when>\n' |