# HG changeset patch
# User iuc
# Date 1655319604 0
# Node ID 31812e7a1315a6f3e69827ee40fce3372fb5d2f9
# Parent  ded48b36f3b7118629548b23d6621a94602d13c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit ecebab288909d75a9f6e86d34a5c85e246678ab2

diff -r ded48b36f3b7 -r 31812e7a1315 macros.xml
--- a/macros.xml	Mon Jun 08 13:09:53 2020 -0400
+++ b/macros.xml	Wed Jun 15 19:00:04 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.19.0</token>
+    <token name="@VERSION@">2.22.0</token>
 
     <xml name="requirements">
         <requirements>
diff -r ded48b36f3b7 -r 31812e7a1315 mlst.xml
--- a/mlst.xml	Mon Jun 08 13:09:53 2020 -0400
+++ b/mlst.xml	Wed Jun 15 19:00:04 2022 +0000
@@ -1,8 +1,10 @@
 <tool id="mlst" name="MLST" version="@VERSION@">
-    <description>Scans genomes against PubMLST schemes.</description>
+    <description>Scans genomes against PubMLST schemes</description>
+    <xrefs>
+        <xref type="bio.tools">mlst</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
-
         <xml name="legacy_param">
             <param argument="--legacy" type="boolean" truevalue="--legacy" falsevalue="" checked="true" label="Include allele header" help="Include allele header row in output table (requires scheme to be set)" />
         </xml>
@@ -78,6 +80,7 @@
                     </when>
                     <when value="list">
                         <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
+                            <option value="aactinomycetemcomitans">aactinomycetemcomitans</option>
                             <option value="abaumannii">abaumannii</option>
                             <option value="abaumannii_2">abaumannii_2</option>
                             <option value="achromobacter">achromobacter</option>
@@ -87,85 +90,97 @@
                             <option value="bbacilliformis">bbacilliformis</option>
                             <option value="bcc">bcc</option>
                             <option value="bcereus">bcereus</option>
-                            <option value="bhampsonii">bhampsonii</option>
+                            <option value="bfragilis">bfragilis</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="blicheniformis_14">blicheniformis_14</option>
+                            <option value="bordetella_3">bordetella_3</option>
                             <option value="borrelia">borrelia</option>
-                            <option value="bpilosicoli">bpilosicoli</option>
                             <option value="bpseudomallei">bpseudomallei</option>
                             <option value="brachyspira">brachyspira</option>
+                            <option value="brachyspira_2">brachyspira_2</option>
+                            <option value="brachyspira_3">brachyspira_3</option>
+                            <option value="brachyspira_4">brachyspira_4</option>
+                            <option value="brachyspira_5">brachyspira_5</option>
                             <option value="brucella">brucella</option>
                             <option value="bsubtilis">bsubtilis</option>
+                            <option value="bwashoensis">bwashoensis</option>
                             <option value="campylobacter">campylobacter</option>
+                            <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option>
+                            <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option>
+                            <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option>
+                            <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option>
+                            <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option>
+                            <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option>
+                            <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option>
+                            <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option>
+                            <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</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="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="cperfringens">cperfringens</option>
                             <option value="cronobacter">cronobacter</option>
                             <option value="csepticum">csepticum</option>
-                            <option value="csputorum">csputorum</option>
-                            <option value="cupsaliensis">cupsaliensis</option>
+                            <option value="diphtheria_3">diphtheria_3</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="ecoli_achtman_4">ecoli_achtman_4</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="gallibacterium">gallibacterium</option>
+                            <option value="geotrichum">geotrichum</option>
                             <option value="hcinaedi">hcinaedi</option>
+                            <option value="helicobacter">helicobacter</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="kkingae">kkingae</option>
+                            <option value="kingella">kingella</option>
+                            <option value="klebsiella">klebsiella</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="liberibacter">liberibacter</option>
+                            <option value="listeria_2">listeria_2</option>
+                            <option value="llactis_phage">llactis_phage</option>
                             <option value="lsalivarius">lsalivarius</option>
                             <option value="mabscessus">mabscessus</option>
                             <option value="magalactiae">magalactiae</option>
-                            <option value="mbovis">mbovis</option>
+                            <option value="manserisalpingitidis">manserisalpingitidis</option>
+                            <option value="mbovis_2">mbovis_2</option>
                             <option value="mcanis">mcanis</option>
                             <option value="mcaseolyticus">mcaseolyticus</option>
-                            <option value="mcatarrhalis">mcatarrhalis</option>
+                            <option value="mcatarrhalis_achtman_6">mcatarrhalis_achtman_6</option>
+                            <option value="mflocculare">mflocculare</option>
+                            <option value="mgallisepticum">mgallisepticum</option>
+                            <option value="mgallisepticum_2">mgallisepticum_2</option>
                             <option value="mhaemolytica">mhaemolytica</option>
+                            <option value="mhominis_3">mhominis_3</option>
                             <option value="mhyopneumoniae">mhyopneumoniae</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="msciuri">msciuri</option>
                             <option value="msynoviae">msynoviae</option>
-                            <option value="mycobacteria">mycobacteria</option>
+                            <option value="mycobacteria_2">mycobacteria_2</option>
                             <option value="neisseria">neisseria</option>
+                            <option value="oralstrep">oralstrep</option>
                             <option value="orhinotracheale">orhinotracheale</option>
                             <option value="otsutsugamushi">otsutsugamushi</option>
-                            <option value="pacnes">pacnes</option>
+                            <option value="pacnes_3">pacnes_3</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="pmultocida">pmultocida</option>
+                            <option value="pmultocida_2">pmultocida_2</option>
                             <option value="ppentosaceus">ppentosaceus</option>
                             <option value="pputida">pputida</option>
                             <option value="psalmonis">psalmonis</option>
@@ -175,23 +190,24 @@
                             <option value="saureus">saureus</option>
                             <option value="sbsec">sbsec</option>
                             <option value="scanis">scanis</option>
+                            <option value="schromogenes">schromogenes</option>
                             <option value="sdysgalactiae">sdysgalactiae</option>
-                            <option value="senterica">senterica</option>
+                            <option value="senterica_achtman_2">senterica_achtman_2</option>
                             <option value="sepidermidis">sepidermidis</option>
                             <option value="sgallolyticus">sgallolyticus</option>
                             <option value="shaemolyticus">shaemolyticus</option>
+                            <option value="shewanella">shewanella</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="staphlugdunensis">staphlugdunensis</option>
                             <option value="sthermophilus">sthermophilus</option>
-                            <option value="sthermophilus_2">sthermophilus_2</option>
                             <option value="streptomyces">streptomyces</option>
+                            <option value="streptothermophilus">streptothermophilus</option>
                             <option value="suberis">suberis</option>
                             <option value="szooepidemicus">szooepidemicus</option>
                             <option value="taylorella">taylorella</option>
@@ -199,15 +215,14 @@
                             <option value="tpallidum">tpallidum</option>
                             <option value="ureaplasma">ureaplasma</option>
                             <option value="vcholerae">vcholerae</option>
-                            <option value="vcholerae2">vcholerae2</option>
+                            <option value="vcholerae_2">vcholerae_2</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="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option>
                             <option value="yruckeri">yruckeri</option>
                         </param>
                         <expand macro="legacy_param" />
diff -r ded48b36f3b7 -r 31812e7a1315 mlst_list.xml
--- a/mlst_list.xml	Mon Jun 08 13:09:53 2020 -0400
+++ b/mlst_list.xml	Wed Jun 15 19:00:04 2022 +0000
@@ -1,5 +1,8 @@
 <tool id="mlst_list" name="MLST List" version="@VERSION@">
-    <description>Lists available schemes for the MLST tool.</description>
+    <description>Lists available schemes for the MLST tool</description>
+    <xrefs>
+        <xref type="bio.tools">mlst</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,7 +10,7 @@
     <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
-        mlst $list_type > "$report"
+        mlst $list_type > '$report'
     ]]></command>
 
     <inputs>