| Previous changeset 5:ded48b36f3b7 (2020-06-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit ecebab288909d75a9f6e86d34a5c85e246678ab2 |
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modified:
macros.xml mlst.xml mlst_list.xml |
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| 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 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.19.0</token> + <token name="@VERSION@">2.22.0</token> <xml name="requirements"> <requirements> |
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| 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 |
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| b'@@ -1,8 +1,10 @@\n <tool id="mlst" name="MLST" version="@VERSION@">\n- <description>Scans genomes against PubMLST schemes.</description>\n+ <description>Scans genomes against PubMLST schemes</description>\n+ <xrefs>\n+ <xref type="bio.tools">mlst</xref>\n+ </xrefs>\n <macros>\n <import>macros.xml</import>\n-\n <xml name="legacy_param">\n <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)" />\n </xml>\n@@ -78,6 +80,7 @@\n </when>\n <when value="list">\n <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">\n+ <option value="aactinomycetemcomitans">aactinomycetemcomitans</option>\n <option value="abaumannii">abaumannii</option>\n <option value="abaumannii_2">abaumannii_2</option>\n <option value="achromobacter">achromobacter</option>\n@@ -87,85 +90,97 @@\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="bfragilis">bfragilis</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="blicheniformis_14">blicheniformis_14</option>\n+ <option value="bordetella_3">bordetella_3</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="brachyspira_2">brachyspira_2</option>\n+ <option value="brachyspira_3">brachyspira_3</option>\n+ <option value="brachyspira_4">brachyspira_4</option>\n+ <option value="brachyspira_5">brachyspira_5</option>\n <option value="brucella">brucella</option>\n <option value="bsubtilis">bsubtilis</option>\n+ <option value="bwashoensis">bwashoensis</option>\n <option value="campylobacter">campylobacter</option>\n+ <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option>\n+ <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option>\n+ <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option>\n+ <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option>\n+ <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option>\n+ <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option>\n+ <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option>\n+ <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option>\n+ <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</option>\n '..b'- <option value="pmultocida_rirdc">pmultocida_rirdc</option>\n+ <option value="pmultocida">pmultocida</option>\n+ <option value="pmultocida_2">pmultocida_2</option>\n <option value="ppentosaceus">ppentosaceus</option>\n <option value="pputida">pputida</option>\n <option value="psalmonis">psalmonis</option>\n@@ -175,23 +190,24 @@\n <option value="saureus">saureus</option>\n <option value="sbsec">sbsec</option>\n <option value="scanis">scanis</option>\n+ <option value="schromogenes">schromogenes</option>\n <option value="sdysgalactiae">sdysgalactiae</option>\n- <option value="senterica">senterica</option>\n+ <option value="senterica_achtman_2">senterica_achtman_2</option>\n <option value="sepidermidis">sepidermidis</option>\n <option value="sgallolyticus">sgallolyticus</option>\n <option value="shaemolyticus">shaemolyticus</option>\n+ <option value="shewanella">shewanella</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="staphlugdunensis">staphlugdunensis</option>\n <option value="sthermophilus">sthermophilus</option>\n- <option value="sthermophilus_2">sthermophilus_2</option>\n <option value="streptomyces">streptomyces</option>\n+ <option value="streptothermophilus">streptothermophilus</option>\n <option value="suberis">suberis</option>\n <option value="szooepidemicus">szooepidemicus</option>\n <option value="taylorella">taylorella</option>\n@@ -199,15 +215,14 @@\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="vcholerae_2">vcholerae_2</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="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option>\n <option value="yruckeri">yruckeri</option>\n </param>\n <expand macro="legacy_param" />\n' |
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| 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 |
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| @@ -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> |