Mercurial > repos > florianbegusch > qiime2_wrappers

changeset 3:eda5df31da55 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Bump version to 2019.4
author florianbegusch
date Wed, 17 Jul 2019 01:53:11 -0400
parents 149432539226
children 71f124e02000
files 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 tool_data/ref_classifier.loc tool_data/ref_taxnonomy.loc tool_data_table_conf.xml.sample
diffstat 9 files changed, 21 insertions(+), 631 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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
--- a/qiime2/.idea/misc.xml	Wed Jul 17 01:49:31 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- a/qiime2/.idea/modules.xml	Wed Jul 17 01:49:31 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- a/qiime2/.idea/qiime2.iml	Wed Jul 17 01:49:31 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- a/qiime2/.idea/vcs.xml	Wed Jul 17 01:49:31 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- a/qiime2/.idea/workspace.xml	Wed Jul 17 01:49:31 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,518 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ChangeListManager">
-    <list default="true" id="b6f0e792-e8ea-43a1-9747-395b6f53af7f" name="Default Changelist" comment="" />
-    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
-    <option name="SHOW_DIALOG" value="false" />
-    <option name="HIGHLIGHT_CONFLICTS" value="true" />
-    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
-    <option name="LAST_RESOLUTION" value="IGNORE" />
-  </component>
-  <component name="FileEditorManager">
-    <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_maturity-index.xml">
-          <provider selected="true" editor-type-id="text-editor" />
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_classify-sklearn.xml">
-          <provider selected="true" editor-type-id="text-editor" />
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_extract-reads.xml">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="735">
-              <caret line="49" column="14" selection-start-line="49" selection-start-column="14" selection-end-line="49" selection-end-column="14" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="true">
-        <entry file="file://$PROJECT_DIR$/qiime_composition_ancom.xml">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="705">
-              <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge.xml">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="435">
-              <caret line="29" selection-start-line="29" selection-end-line="29" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-seqs.xml">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="360">
-              <caret line="24" selection-start-line="24" selection-end-line="24" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-taxa.xml">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="360">
-              <caret line="24" selection-start-line="24" selection-end-line="24" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-denovo.xml">
-          <provider selected="true" editor-type-id="text-editor" />
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-ref.xml">
-          <provider selected="true" editor-type-id="text-editor" />
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/qiime_tools_import.xml">
-          <provider selected="true" editor-type-id="text-editor" />
-        </entry>
-      </file>
-    </leaf>
-  </component>
-  <component name="FindInProjectRecents">
-    <findStrings>
-      <find>anywhere-r</find>
-    </findStrings>
-  </component>
-  <component name="Git.Settings">
-    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$/.." />
-  </component>
-  <component name="IdeDocumentHistory">
-    <option name="CHANGED_PATHS">
-      <list>
-        <option value="$PROJECT_DIR$/qiime_diversity_beta-phylogenetic.xml" />
-        <option value="$PROJECT_DIR$/qiime_feature-classifier_extract-reads.xml" />
-      </list>
-    </option>
-  </component>
-  <component name="ProjectFrameBounds" extendedState="4">
-    <option name="y" value="26" />
-    <option name="width" value="960" />
-    <option name="height" value="1054" />
-  </component>
-  <component name="ProjectLevelVcsManager" settingsEditedManually="true" />
-  <component name="ProjectView">
-    <navigator proportions="" version="1">
-      <foldersAlwaysOnTop value="true" />
-    </navigator>
-    <panes>
-      <pane id="ProjectPane">
-        <subPane>
-          <expand>
-            <path>
-              <item name="qiime2" type="b2602c69:ProjectViewProjectNode" />
-              <item name="qiime2" type="462c0819:PsiDirectoryNode" />
-            </path>
-          </expand>
-          <select />
-        </subPane>
-      </pane>
-      <pane id="Scope" />
-      <pane id="PackagesPane" />
-    </panes>
-  </component>
-  <component name="PropertiesComponent">
-    <property name="last_opened_file_path" value="$PROJECT_DIR$" />
-    <property name="project.structure.last.edited" value="Problems" />
-    <property name="project.structure.proportion" value="0.15" />
-    <property name="project.structure.side.proportion" value="0.2" />
-    <property name="settings.editor.selected.configurable" value="reference.settingsdialog.IDE.editor.colors.XML" />
-  </component>
-  <component name="RunDashboard">
-    <option name="ruleStates">
-      <list>
-        <RuleState>
-          <option name="name" value="ConfigurationTypeDashboardGroupingRule" />
-        </RuleState>
-        <RuleState>
-          <option name="name" value="StatusDashboardGroupingRule" />
-        </RuleState>
-      </list>
-    </option>
-  </component>
-  <component name="RunManager">
-    <configuration default="true" type="Applet">
-      <option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy" />
-      <method v="2">
-        <option name="Make" enabled="true" />
-      </method>
-    </configuration>
-    <configuration default="true" type="Application" factoryName="Application">
-      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
-      <method v="2">
-        <option name="Make" enabled="true" />
-      </method>
-    </configuration>
-    <configuration default="true" type="JUnit" factoryName="JUnit">
-      <option name="TEST_OBJECT" value="class" />
-      <option name="WORKING_DIRECTORY" value="$MODULE_DIR$" />
-      <method v="2">
-        <option name="Make" enabled="true" />
-      </method>
-    </configuration>
-    <configuration default="true" type="TestNG">
-      <option name="TEST_OBJECT" value="CLASS" />
-      <option name="WORKING_DIRECTORY" value="$MODULE_DIR$" />
-      <properties />
-      <listeners />
-      <method v="2">
-        <option name="Make" enabled="true" />
-      </method>
-    </configuration>
-    <configuration default="true" type="#org.jetbrains.idea.devkit.run.PluginConfigurationType">
-      <module name="" />
-      <option name="VM_PARAMETERS" value="-Xmx512m -Xms256m -XX:MaxPermSize=250m -ea" />
-      <option name="PROGRAM_PARAMETERS" />
-      <predefined_log_file enabled="true" id="idea.log" />
-      <method v="2">
-        <option name="Make" enabled="true" />
-      </method>
-    </configuration>
-  </component>
-  <component name="SvnConfiguration">
-    <configuration />
-  </component>
-  <component name="TaskManager">
-    <task active="true" id="Default" summary="Default task">
-      <changelist id="b6f0e792-e8ea-43a1-9747-395b6f53af7f" name="Default Changelist" comment="" />
-      <created>1562958108875</created>
-      <option name="number" value="Default" />
-      <option name="presentableId" value="Default" />
-      <updated>1562958108875</updated>
-    </task>
-    <servers />
-  </component>
-  <component name="ToolWindowManager">
-    <frame x="0" y="26" width="960" height="1054" extended-state="4" />
-    <editor active="true" />
-    <layout>
-      <window_info active="true" content_ui="combo" id="Project" order="0" sideWeight="0.43736503" visible="true" weight="0.24836601" />
-      <window_info id="Structure" order="1" sideWeight="0.562635" side_tool="true" visible="true" weight="0.24836601" />
-      <window_info id="Nl-Palette" order="2" />
-      <window_info id="Capture Tool" order="3" />
-      <window_info id="Designer" order="4" />
-      <window_info id="UI Designer" order="5" />
-      <window_info id="Image Layers" order="6" />
-      <window_info id="Captures" order="7" sideWeight="0.45717037" weight="0.32995737" />
-      <window_info id="Favorites" order="8" sideWeight="0.54282963" side_tool="true" weight="0.32995737" />
-      <window_info id="Build Variants" order="9" sideWeight="0.54282963" side_tool="true" weight="0.32995737" />
-      <window_info anchor="bottom" id="Message" order="0" />
-      <window_info anchor="bottom" id="Find" order="1" sideWeight="0.49573562" weight="0.3282002" />
-      <window_info anchor="bottom" id="Run" order="2" sideWeight="0.4953125" weight="0.29162657" />
-      <window_info anchor="bottom" id="Debug" order="3" sideWeight="0.49479166" weight="0.39942253" />
-      <window_info anchor="bottom" id="Cvs" order="4" weight="0.25" />
-      <window_info anchor="bottom" id="Inspection" order="5" weight="0.4" />
-      <window_info anchor="bottom" id="TODO" order="6" weight="0.32916266" />
-      <window_info anchor="bottom" id="Event Log" order="7" sideWeight="0.5042644" side_tool="true" weight="0.3282002" />
-      <window_info anchor="bottom" id="Messages" order="8" sideWeight="0.49791667" weight="0.32627526" />
-      <window_info anchor="bottom" id="Version Control" order="9" weight="0.3282002" />
-      <window_info anchor="bottom" id="Terminal" order="10" weight="0.3282002" />
-      <window_info anchor="bottom" id="Android Monitor" order="11" weight="0.3298077" />
-      <window_info anchor="right" id="Commander" order="0" weight="0.4" />
-      <window_info anchor="right" id="Ant Build" order="1" weight="0.25" />
-      <window_info anchor="right" content_ui="combo" id="Hierarchy" order="2" weight="0.25" />
-      <window_info anchor="right" id="Palette" order="3" />
-      <window_info anchor="right" id="Properties" order="4" />
-      <window_info anchor="right" id="Android Model" order="5" side_tool="true" />
-      <window_info anchor="right" id="Palette&#9;" order="6" />
-      <window_info anchor="right" id="Capture Analysis" order="7" />
-      <window_info anchor="right" id="Gradle" order="8" />
-      <window_info anchor="right" id="Theme Preview" order="9" />
-      <window_info anchor="right" id="Maven Projects" order="10" />
-      <window_info anchor="right" id="Preview" order="11" />
-      <window_info anchor="right" id="Maven" order="12" />
-    </layout>
-  </component>
-  <component name="editorHistoryManager">
-    <entry file="file://$PROJECT_DIR$/qiime_feature-table_summarize.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-233" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_add-pseudocount.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-table_tabulate-seqs.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_assign-ids.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="585">
-          <caret line="42" column="39" selection-start-line="42" selection-start-column="39" selection-end-line="42" selection-end-column="39" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_balance-taxonomy.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-1193" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_correlation-clustering.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-38" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_dendrogram-heatmap.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-225" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_gradient-clustering.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-45" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_lme-regression.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-405" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_gneiss_ols-regression.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_first-differences.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_first-distances.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_linear-mixed-effects.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_nmit.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="240">
-          <caret line="16" column="12" lean-forward="true" selection-start-line="16" selection-start-column="12" selection-end-line="16" selection-end-column="12" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_pairwise-differences.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-360" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_pairwise-distances.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_longitudinal_volatility.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_metadata_distance-matrix.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-173" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_metadata_tabulate.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="225">
-          <caret line="18" column="5" lean-forward="true" selection-start-line="18" selection-start-column="5" selection-end-line="18" selection-end-column="65" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_phylogeny_fasttree.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_phylogeny_filter-table.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-23" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_phylogeny_midpoint-root.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_quality-control_evaluate-composition.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_quality-control_evaluate-seqs.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-368" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_quality-control_exclude-seqs.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_quality-filter_q-score.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-53" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_quality-filter_q-score-joined.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_classify-samples.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_regress-samples.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-1133">
-          <caret line="52" column="11" lean-forward="true" selection-start-line="52" selection-start-column="11" selection-end-line="52" selection-end-column="11" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_taxa_barplot.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_taxa_collapse.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_taxa_filter-seqs.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="105">
-          <caret line="10" selection-start-line="10" selection-end-line="16" selection-end-column="11" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_tools_export.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_tools_export_collection.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_tools_export_paired_collection.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_cluster-features-de-novo.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-398" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_cluster-features-open-reference.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-90" />
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_cluster-features-closed-reference.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="690">
-          <caret line="46" column="13" selection-start-line="46" selection-start-column="13" selection-end-line="46" selection-end-column="13" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_dereplicate-sequences.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_join-pairs.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="1665">
-          <caret line="111" selection-start-line="111" selection-end-line="111" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_taxa_filter-table.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_maturity-index.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_classify-sklearn.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-denovo.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_vsearch_uchime-ref.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_tools_import.xml">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_extract-reads.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="735">
-          <caret line="49" column="14" selection-start-line="49" selection-start-column="14" selection-end-line="49" selection-end-column="14" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="435">
-          <caret line="29" selection-start-line="29" selection-end-line="29" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-seqs.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="360">
-          <caret line="24" selection-start-line="24" selection-end-line="24" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-taxa.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="360">
-          <caret line="24" selection-start-line="24" selection-end-line="24" />
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/qiime_composition_ancom.xml">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="705">
-          <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" />
-        </state>
-      </provider>
-    </entry>
-  </component>
-  <component name="masterDetails">
-    <states>
-      <state key="GlobalLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="JdkListConfigurable.UI">
-        <settings>
-          <last-edited>1.8</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectJDKs.UI">
-        <settings>
-          <last-edited>1.8</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-    </states>
-  </component>
-</project>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_classifier.loc	Wed Jul 17 01:53:11 2019 -0400
@@ -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
+#
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_taxnonomy.loc	Wed Jul 17 01:53:11 2019 -0400
@@ -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
+#
+
--- /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
@@ -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>
+