| Previous changeset 2:149432539226 (2019-07-17) Next changeset 4:71f124e02000 (2019-08-13) |
|
Commit message:
Bump version to 2019.4 |
|
added:
tool_data/ref_classifier.loc tool_data/ref_taxnonomy.loc tool_data_table_conf.xml.sample |
|
removed:
qiime2/.idea/markdown-navigator/profiles_settings.xml qiime2/.idea/misc.xml qiime2/.idea/modules.xml qiime2/.idea/qiime2.iml qiime2/.idea/vcs.xml qiime2/.idea/workspace.xml |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/markdown-navigator/profiles_settings.xml --- a/qiime2/.idea/markdown-navigator/profiles_settings.xml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -<component name="MarkdownNavigator.ProfileManager"> - <settings default="" pdf-export="" plain-text-search-scope="Project Files" /> -</component> \ No newline at end of file |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/misc.xml --- a/qiime2/.idea/misc.xml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,87 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project version="4"> - <component name="MarkdownProjectSettings" wasCopied="true"> - <PreviewSettings splitEditorLayout="SPLIT" splitEditorPreview="PREVIEW" useGrayscaleRendering="false" zoomFactor="1.0" maxImageWidth="0" showGitHubPageIfSynced="false" allowBrowsingInPreview="false" synchronizePreviewPosition="true" highlightPreviewType="NONE" highlightFadeOut="5" highlightOnTyping="true" synchronizeSourcePosition="true" verticallyAlignSourceAndPreviewSyncPosition="true" showSearchHighlightsInPreview="false" showSelectionInPreview="true" openRemoteLinks="true" replaceUnicodeEmoji="false" lastLayoutSetsDefault="false"> - <PanelProvider> - <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.panel" providerName="Default - Swing" /> - </PanelProvider> - </PreviewSettings> - <ParserSettings gitHubSyntaxChange="false" emojiShortcuts="1" emojiImages="0"> - <PegdownExtensions> - <option name="ABBREVIATIONS" value="false" /> - <option name="ANCHORLINKS" value="true" /> - <option name="ASIDE" value="false" /> - <option name="ATXHEADERSPACE" value="true" /> - <option name="AUTOLINKS" value="false" /> - <option name="DEFINITIONS" value="false" /> - <option name="DEFINITION_BREAK_DOUBLE_BLANK_LINE" value="false" /> - <option name="FENCED_CODE_BLOCKS" value="true" /> - <option name="FOOTNOTES" value="false" /> - <option name="HARDWRAPS" value="false" /> - <option name="HTML_DEEP_PARSER" value="false" /> - <option name="INSERTED" value="false" /> - <option name="QUOTES" value="false" /> - <option name="RELAXEDHRULES" value="true" /> - <option name="SMARTS" value="false" /> - <option name="STRIKETHROUGH" value="true" /> - <option name="SUBSCRIPT" value="false" /> - <option name="SUPERSCRIPT" value="false" /> - <option name="SUPPRESS_HTML_BLOCKS" value="false" /> - <option name="SUPPRESS_INLINE_HTML" value="false" /> - <option name="TABLES" value="true" /> - <option name="TASKLISTITEMS" value="true" /> - <option name="TOC" value="false" /> - <option name="WIKILINKS" value="false" /> - </PegdownExtensions> - <ParserOptions> - <option name="ADMONITION_EXT" value="false" /> - <option name="ATTRIBUTES_EXT" value="false" /> - <option name="COMMONMARK_LISTS" value="true" /> - <option name="DUMMY" value="false" /> - <option name="EMOJI_SHORTCUTS" value="true" /> - <option name="ENUMERATED_REFERENCES_EXT" value="false" /> - <option name="FLEXMARK_FRONT_MATTER" value="false" /> - <option name="GFM_LOOSE_BLANK_LINE_AFTER_ITEM_PARA" value="false" /> - <option name="GFM_TABLE_RENDERING" value="true" /> - <option name="GITBOOK_URL_ENCODING" value="false" /> - <option name="GITHUB_LISTS" value="false" /> - <option name="GITHUB_WIKI_LINKS" value="false" /> - <option name="GITLAB_EXT" value="false" /> - <option name="GITLAB_MATH_EXT" value="false" /> - <option name="GITLAB_MERMAID_EXT" value="false" /> - <option name="HEADER_ID_NON_ASCII_TO_LOWERCASE" value="false" /> - <option name="HEADER_ID_NO_DUPED_DASHES" value="false" /> - <option name="JEKYLL_FRONT_MATTER" value="false" /> - <option name="MACROS_EXT" value="false" /> - <option name="NO_TEXT_ATTRIBUTES" value="false" /> - <option name="PARSE_HTML_ANCHOR_ID" value="false" /> - <option name="PLANTUML_FENCED_CODE" value="false" /> - <option name="PUML_FENCED_CODE" value="false" /> - <option name="SIM_TOC_BLANK_LINE_SPACER" value="true" /> - </ParserOptions> - </ParserSettings> - <HtmlSettings headerTopEnabled="false" headerBottomEnabled="false" bodyTopEnabled="false" bodyBottomEnabled="false" embedUrlContent="false" addPageHeader="true" embedImages="false" embedHttpImages="false" imageUriSerials="false" addDocTypeHtml="true" noParaTags="false" plantUmlConversion="0" mathConversion="0"> - <GeneratorProvider> - <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.generator" providerName="Default Swing HTML Generator" /> - </GeneratorProvider> - <headerTop /> - <headerBottom /> - <bodyTop /> - <bodyBottom /> - </HtmlSettings> - <CssSettings previewScheme="UI_SCHEME" cssUri="" isCssUriEnabled="false" isCssUriSerial="true" isCssTextEnabled="false" isDynamicPageWidth="true"> - <StylesheetProvider> - <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.css" providerName="Default Swing Stylesheet" /> - </StylesheetProvider> - <ScriptProviders /> - <cssText /> - <cssUriHistory /> - </CssSettings> - <AnnotatorSettings targetHasSpaces="true" linkCaseMismatch="true" wikiCaseMismatch="true" wikiLinkHasDashes="true" notUnderWikiHome="true" targetNotWikiPageExt="true" notUnderSourceWikiHome="true" targetNameHasAnchor="true" targetPathHasAnchor="true" wikiLinkHasSlash="true" wikiLinkHasSubdir="true" wikiLinkHasOnlyAnchor="true" linkTargetsWikiHasExt="true" linkTargetsWikiHasBadExt="true" notUnderSameRepo="true" targetNotUnderVcs="false" linkNeedsExt="true" linkHasBadExt="true" linkTargetNeedsExt="true" linkTargetHasBadExt="true" wikiLinkNotInWiki="true" imageTargetNotInRaw="true" repoRelativeAcrossVcsRoots="true" multipleWikiTargetsMatch="true" unresolvedLinkReference="true" linkIsIgnored="true" anchorIsIgnored="true" anchorIsUnresolved="true" anchorLineReferenceIsUnresolved="true" anchorLineReferenceFormat="true" anchorHasDuplicates="true" abbreviationDuplicates="true" abbreviationNotUsed="true" attributeIdDuplicateDefinition="true" attributeIdNotUsed="true" footnoteDuplicateDefinition="true" footnoteUnresolved="true" footnoteDuplicates="true" footnoteNotUsed="true" macroDuplicateDefinition="true" macroUnresolved="true" macroDuplicates="true" macroNotUsed="true" referenceDuplicateDefinition="true" referenceUnresolved="true" referenceDuplicates="true" referenceNotUsed="true" referenceUnresolvedNumericId="true" enumRefDuplicateDefinition="true" enumRefUnresolved="true" enumRefDuplicates="true" enumRefNotUsed="true" enumRefLinkUnresolved="true" enumRefLinkDuplicates="true" simTocUpdateNeeded="true" simTocTitleSpaceNeeded="true" /> - <HtmlExportSettings updateOnSave="false" parentDir="" targetDir="" cssDir="css" scriptDir="js" plainHtml="false" imageDir="" copyLinkedImages="false" imageUniquifyType="0" targetPathType="2" targetExt="" useTargetExt="false" noCssNoScripts="false" useElementStyleAttribute="false" linkToExportedHtml="true" exportOnSettingsChange="true" regenerateOnProjectOpen="false" linkFormatType="HTTP_ABSOLUTE" /> - <LinkMapSettings> - <textMaps /> - </LinkMapSettings> - </component> - <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" project-jdk-name="1.8" project-jdk-type="JavaSDK" /> -</project> \ No newline at end of file |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/modules.xml --- a/qiime2/.idea/modules.xml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project version="4"> - <component name="ProjectModuleManager"> - <modules> - <module fileurl="file://$PROJECT_DIR$/.idea/qiime2.iml" filepath="$PROJECT_DIR$/.idea/qiime2.iml" /> - </modules> - </component> -</project> \ No newline at end of file |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/qiime2.iml --- a/qiime2/.idea/qiime2.iml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<module type="JAVA_MODULE" version="4"> - <component name="NewModuleRootManager" inherit-compiler-output="true"> - <exclude-output /> - <content url="file://$MODULE_DIR$" /> - <orderEntry type="inheritedJdk" /> - <orderEntry type="sourceFolder" forTests="false" /> - </component> -</module> \ No newline at end of file |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/vcs.xml --- a/qiime2/.idea/vcs.xml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project version="4"> - <component name="VcsDirectoryMappings"> - <mapping directory="$PROJECT_DIR$/.." vcs="Git" /> - </component> -</project> \ No newline at end of file |
| b |
| diff -r 149432539226 -r eda5df31da55 qiime2/.idea/workspace.xml --- a/qiime2/.idea/workspace.xml Wed Jul 17 01:49:31 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,518 +0,0 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<project version="4">\n- <component name="ChangeListManager">\n- <list default="true" id="b6f0e792-e8ea-43a1-9747-395b6f53af7f" name="Default Changelist" comment="" />\n- <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />\n- <option name="SHOW_DIALOG" value="false" />\n- <option name="HIGHLIGHT_CONFLICTS" value="true" />\n- <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />\n- <option name="LAST_RESOLUTION" value="IGNORE" />\n- </component>\n- <component name="FileEditorManager">\n- <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_maturity-index.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_classify-sklearn.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_extract-reads.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="735">\n- <caret line="49" column="14" selection-start-line="49" selection-start-column="14" selection-end-line="49" selection-end-column="14" />\n- </state>\n- </provider>\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="true">\n- <entry file="file://$PROJECT_DIR$/qiime_composition_ancom.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="705">\n- <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" />\n- </state>\n- </provider>\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="435">\n- <caret line="29" selection-start-line="29" selection-end-line="29" />\n- </state>\n- </provider>\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-seqs.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="360">\n- <caret line="24" selection-start-line="24" selection-end-line="24" />\n- </state>\n- </provider>\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-taxa.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="360">\n- <caret line="24" selection-start-line="24" selection-end-line="24" />\n- </state>\n- </provider>\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-denovo.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-ref.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- </file>\n- <file pinned="false" current-in-tab="false">\n- <entry file="file://$PROJECT_DIR$/qiime_tools_import.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- </file>\n- </leaf>\n- <'..b'>\n- <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_maturity-index.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_classify-sklearn.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-denovo.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-ref.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_tools_import.xml">\n- <provider selected="true" editor-type-id="text-editor" />\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_extract-reads.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="735">\n- <caret line="49" column="14" selection-start-line="49" selection-start-column="14" selection-end-line="49" selection-end-column="14" />\n- </state>\n- </provider>\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="435">\n- <caret line="29" selection-start-line="29" selection-end-line="29" />\n- </state>\n- </provider>\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-seqs.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="360">\n- <caret line="24" selection-start-line="24" selection-end-line="24" />\n- </state>\n- </provider>\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-taxa.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="360">\n- <caret line="24" selection-start-line="24" selection-end-line="24" />\n- </state>\n- </provider>\n- </entry>\n- <entry file="file://$PROJECT_DIR$/qiime_composition_ancom.xml">\n- <provider selected="true" editor-type-id="text-editor">\n- <state relative-caret-position="705">\n- <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" />\n- </state>\n- </provider>\n- </entry>\n- </component>\n- <component name="masterDetails">\n- <states>\n- <state key="GlobalLibrariesConfigurable.UI">\n- <settings>\n- <splitter-proportions>\n- <option name="proportions">\n- <list>\n- <option value="0.2" />\n- </list>\n- </option>\n- </splitter-proportions>\n- </settings>\n- </state>\n- <state key="JdkListConfigurable.UI">\n- <settings>\n- <last-edited>1.8</last-edited>\n- <splitter-proportions>\n- <option name="proportions">\n- <list>\n- <option value="0.2" />\n- </list>\n- </option>\n- </splitter-proportions>\n- </settings>\n- </state>\n- <state key="ProjectJDKs.UI">\n- <settings>\n- <last-edited>1.8</last-edited>\n- <splitter-proportions>\n- <option name="proportions">\n- <list>\n- <option value="0.2" />\n- </list>\n- </option>\n- </splitter-proportions>\n- </settings>\n- </state>\n- <state key="ProjectLibrariesConfigurable.UI">\n- <settings>\n- <splitter-proportions>\n- <option name="proportions">\n- <list>\n- <option value="0.2" />\n- </list>\n- </option>\n- </splitter-proportions>\n- </settings>\n- </state>\n- </states>\n- </component>\n-</project>\n\\ No newline at end of file\n' |
| b |
| diff -r 149432539226 -r eda5df31da55 tool_data/ref_classifier.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data/ref_classifier.loc Wed Jul 17 01:53:11 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +#<unique_id> <name> <database_caption> <qza_file_path> +# +#For each reference database, you need to download the qza file in qiime path +# + |
| b |
| diff -r 149432539226 -r eda5df31da55 tool_data/ref_taxnonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data/ref_taxnonomy.loc Wed Jul 17 01:53:11 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +#<unique_id> <name> <database_caption> <qza_file_path> +# +#For each reference database, you need to download the qza file in qiime path +# + |
| b |
| diff -r 149432539226 -r eda5df31da55 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jul 17 01:53:11 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +<tables> + <table name="taxonomy_fp" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool_data/ref_taxnonomy.loc" /> + </table> + <table name="classifier_fp" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/ref_classifier.loc" /> + </table> +</tables> + |