changeset 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 ded48b36f3b7
files macros.xml mlst.xml
diffstat 2 files changed, 122 insertions(+), 121 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Oct 15 07:41:48 2018 -0400
+++ b/macros.xml	Sat Dec 29 13:30:32 2018 -0500
@@ -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>
 
--- 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>