Mercurial > repos > iuc > mlst
changeset 6:31812e7a1315 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit ecebab288909d75a9f6e86d34a5c85e246678ab2
| author | iuc |
|---|---|
| date | Wed, 15 Jun 2022 19:00:04 +0000 |
| parents | ded48b36f3b7 |
| children | |
| files | macros.xml mlst.xml mlst_list.xml |
| diffstat | 3 files changed, 59 insertions(+), 41 deletions(-) [+] |
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--- 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>
--- 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" />
--- 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>