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sequenceanalysis.xml
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2884 lines (2876 loc) · 127 KB
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<tables xsi:schemaLocation="http://labkey.org/data/xml ..\..\..\..\schemas\tableInfo.xsd" xmlns="http://labkey.org/data/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<table tableName="barcodes" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>DNA Barcodes</tableTitle>
<pkColumnName>tag_name</pkColumnName>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<columns>
<column columnName="tag_name">
<nullable>false</nullable>
<isKeyField>true</isKeyField>
</column>
<column columnName="sequence">
<nullable>false</nullable>
<inputType>textarea</inputType>
<description>This should be the forward orientation of the sequence, as it appears in the adapter sequence</description>
</column>
<column columnName="reverse_complement">
<nullable>true</nullable>
<inputType>textarea</inputType>
<isUserEditable>false</isUserEditable>
<description>The reverse complement of the sequence</description>
</column>
<column columnName="group_name">
<nullable>false</nullable>
</column>
<column columnName="createdby">
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<!--<isHidden>true</isHidden>-->
</column>
</columns>
</table>
<table tableName="sequence_platforms" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>Sequence Platforms</tableTitle>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<pkColumnName>platform</pkColumnName>
<columns>
<column columnName="platform">
</column>
<column columnName="aliases">
</column>
</columns>
</table>
<table tableName="sequence_applications" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>Sequence Applications</tableTitle>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<pkColumnName>application</pkColumnName>
<columns>
<column columnName="application">
</column>
</columns>
</table>
<table tableName="sequence_chemistries" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>Sequence Chemistries</tableTitle>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<pkColumnName>chemistry</pkColumnName>
<columns>
<column columnName="chemistry">
</column>
</columns>
</table>
<table tableName="dna_loci" tableDbType="TABLE">
<auditLogging>DETAILED</auditLogging>
<tableTitle>DNA Loci</tableTitle>
<pkColumnName>locus</pkColumnName>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<columns>
<column columnName="locus">
</column>
<column columnName="regexp">
<nullable>true</nullable>
</column>
</columns>
</table>
<table tableName="ref_nt_category" tableDbType="TABLE">
<auditLogging>DETAILED</auditLogging>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<tableTitle>Reference NT Category</tableTitle>
<pkColumnName>category</pkColumnName>
<columns>
<column columnName="category">
</column>
</columns>
</table>
<table tableName="dna_region" tableDbType="TABLE">
<auditLogging>DETAILED</auditLogging>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<tableTitle>DNA Regions</tableTitle>
<pkColumnName>region</pkColumnName>
<columns>
<column columnName="region">
</column>
</columns>
</table>
<table tableName="sequence_coverage" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
<tableTitle>Sequence Coverage</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&query.queryName=Sequence_Coverage&keyField=rowid&key=${rowid}</tableUrl>
<insertUrl></insertUrl>
<importUrl></importUrl>
<deleteUrl></deleteUrl>
<updateUrl></updateUrl>
<titleColumn>adj_depth</titleColumn>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
<columnTitle>Read Id</columnTitle>
</column>
<column columnName="analysis_id">
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>sequence_analyses</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="ref_nt_id">
<columnTitle>Ref NT Id</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_nt_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="ref_nt_position">
<columnTitle>Ref NT Position</columnTitle>
</column>
<column columnName="ref_nt_insert_index">
<columnTitle>Ref NT Index</columnTitle>
</column>
<column columnName="depth">
<nullable>true</nullable>
</column>
<column columnName="adj_depth">
<nullable>true</nullable>
<columnTitle>Adjusted Depth</columnTitle>
</column>
<column columnName="wt">
<nullable>true</nullable>
<columnTitle>Total WT</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="total_n">
<nullable>true</nullable>
<columnTitle>Total Ns</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="total_a">
<columnTitle>Total As</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="total_t">
<columnTitle>Total Ts</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="total_g">
<displayWidth>30</displayWidth>
<columnTitle>Total Gs</columnTitle>
</column>
<column columnName="total_c">
<columnTitle>Total Cs</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="total_del">
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_a">
<columnTitle>Avg Qual of As</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_g">
<columnTitle>Avg Qual of Gs</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_t">
<columnTitle>Avg Qual of Ts</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_c">
<columnTitle>Avg Qual of Cs</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_n">
<columnTitle>Avg Qual of Ns</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="avgqual_del">
<columnTitle>Avg Qual of Dels</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_a">
<columnTitle>P-value of As</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_g">
<columnTitle>P-value of Gs</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_t">
<columnTitle>P-value of Ts</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_c">
<columnTitle>P-value of Cs</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_n">
<columnTitle>P-value of Ns</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="pvalue_del">
<columnTitle>P-value of Dels</columnTitle>
<displayWidth>30</displayWidth>
</column>
<column columnName="container">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="createdby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<!--<isHidden>true</isHidden>-->
</column>
</columns>
</table>
<table tableName="ref_aa_sequences" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.ldk.query.BuiltInColumnsCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Reference AA Sequences</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&query.queryName=Ref_AA_Sequences&keyField=rowid&key=${rowid}</tableUrl>
<importUrl></importUrl>
<insertUrl></insertUrl>
<deleteUrl></deleteUrl>
<updateUrl></updateUrl>
<titleColumn>name</titleColumn>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
<columnTitle>AA Sequence Id</columnTitle>
</column>
<column columnName="ref_nt_id">
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_nt_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
<columnTitle>Ref NT Id</columnTitle>
</column>
<column columnName="name">
<displayWidth>100</displayWidth>
</column>
<column columnName="exons">
<nullable>false</nullable>
</column>
<column columnName="isComplement">
<columnTitle>Is Reverse Complement?</columnTitle>
</column>
<column columnName="start_location">
<nullable>true</nullable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
</column>
<column columnName="sequence">
<displayWidth>200</displayWidth>
<inputType>textarea</inputType>
<columnTitle>AA Sequence</columnTitle>
</column>
<column columnName="comments">
<nullable>true</nullable>
<inputType>textarea</inputType>
</column>
<column columnName="status">
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="container">
</column>
<column columnName="createdby">
<nullable>true</nullable>
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
</columns>
<buttonBarOptions includeStandardButtons="false">
<includeScript>laboratory.context</includeScript>
<includeScript>sequenceanalysis/sequenceAnalysis</includeScript>
<item text="Grid Views">
<originalText>Grid Views</originalText>
</item>
<item text="Delete" permission="DELETE" requiresSelection="true" insertBefore="Export" iconCls="trash">
<onClick>SequenceAnalysis.Buttons.deleteTable(dataRegionName);</onClick>
</item>
<item text="Export">
<originalText>Export</originalText>
</item>
<item text="Print">
<originalText>Print</originalText>
</item>
</buttonBarOptions>
</table>
<table tableName="dna_adapters" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>DNA Adapters</tableTitle>
<pkColumnName>name</pkColumnName>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<columns>
<column columnName="name">
<nullable>false</nullable>
<isKeyField>true</isKeyField>
</column>
<column columnName="group_name">
<nullable>false</nullable>
</column>
<column columnName="sequence">
<nullable>false</nullable>
<scale>225</scale>
</column>
</columns>
</table>
<table tableName="sequence_analyses" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.sequenceanalysis.query.AnalysesTableCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Sequence Analysis Runs</tableTitle>
<pkColumnName>rowid</pkColumnName>
<titleColumn>rowid</titleColumn>
<tableUrl>/sequenceanalysis/sequenceAnalysisDetails.view?id=${rowid}</tableUrl>
<insertUrl></insertUrl>
<importUrl></importUrl>
<deleteUrl></deleteUrl>
<updateUrl>/ldk/manageRecord.view?schemaName=sequenceanalysis&query.queryName=Sequence_Analyses&keyField=rowid&key=${rowid}</updateUrl>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
<columnTitle>Analysis Id</columnTitle>
</column>
<column columnName="type">
<nullable>true</nullable>
<columnTitle>Analysis Type</columnTitle>
</column>
<column columnName="description">
<columnTitle>Description</columnTitle>
<inputType>textarea</inputType>
</column>
<column columnName="synopsis">
<columnTitle>Synopsis</columnTitle>
<isUserEditable>false</isUserEditable>
</column>
<column columnName="runid">
<nullable>true</nullable>
<columnTitle>Run</columnTitle>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>true</shownInUpdateView>
<isUserEditable>false</isUserEditable>
<fk>
<fkDbSchema>exp</fkDbSchema>
<fkTable>runs</fkTable>
<fkColumnName>RowId</fkColumnName>
<fkDisplayColumnName>RowId</fkDisplayColumnName>
</fk>
<url>/experiment/showRunGraphDetail.view?rowId=${runid}</url>
</column>
<column columnName="readset">
<nullable>true</nullable>
<columnTitle>Readset</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>sequence_readsets</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
<!--<url>/query/executeQuery.view?-->
<!--schemaName=sequenceanalysis&-->
<!--query.queryName=sequence_readsets&-->
<!--query.rowid~eq=${readset}&-->
<!--</url>-->
</column>
<column columnName="alignmentfile">
<nullable>true</nullable>
<isUserEditable>false</isUserEditable>
<columnTitle>Alignment File</columnTitle>
<fk>
<fkDbSchema>exp</fkDbSchema>
<fkTable>data</fkTable>
<fkColumnName>RowId</fkColumnName>
</fk>
</column>
<!--TODO: deprecate in favor of this library_id-->
<column columnName="reference_library">
<nullable>true</nullable>
<isHidden>true</isHidden>
<columnTitle>Reference Genome FASTA</columnTitle>
<fk>
<fkDbSchema>exp</fkDbSchema>
<fkTable>data</fkTable>
<fkColumnName>RowId</fkColumnName>
</fk>
</column>
<column columnName="library_id">
<columnTitle>Reference Genome</columnTitle>
<nullable>true</nullable>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>reference_libraries</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="container">
</column>
<column columnName="createdby">
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<isHidden>true</isHidden>
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="sra_accession">
<nullable>true</nullable>
<columnTitle>SRA Run</columnTitle>
<url>https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=${sra_accession}</url>
</column>
<column columnName="metrics" wrappedColumnName="rowid">
<columnTitle>Quality Metrics</columnTitle>
<isUnselectable>true</isUnselectable>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>quality_metrics_analyses_pivoted</fkTable>
<fkColumnName>analysis_id</fkColumnName>
</fk>
</column>
</columns>
<buttonBarOptions includeStandardButtons="false">
<includeScript>laboratory.context</includeScript>
<includeScript>sequenceanalysis/sequenceAnalysis</includeScript>
<item text="Grid Views">
<originalText>Grid Views</originalText>
</item>
<item text="Delete" permission="DELETE" requiresSelection="true" insertBefore="Export" iconCls="trash">
<onClick>SequenceAnalysis.Buttons.deleteTable(dataRegionName);</onClick>
</item>
<item text="Export">
<originalText>Export</originalText>
</item>
<item text="Print">
<originalText>Print</originalText>
</item>
<item insertPosition="end" requiresSelection="false" text="More Actions" iconCls="ellipsis-h">
<item text="Analyze Selected BAMs">
<onClick>SequenceAnalysis.Buttons.performAnalysis(dataRegionName)</onClick>
</item>
<item text="View FASTQC Report">
<onClick>SequenceAnalysis.Buttons.generateFastQcForAnalysis(dataRegionName);</onClick>
</item>
<item text="View Quality Metrics">
<onClick>SequenceAnalysis.Buttons.viewQualityMetrics(dataRegionName, 'analysis_id');</onClick>
</item>
<item text="Download Sequence Files">
<onClick>SequenceAnalysis.window.RunExportWindow.downloadFilesForAnalysis(dataRegionName);</onClick>
</item>
<item text="Alignment Reports">
<item text="Matching Haplotypes">
<onClick>SequenceAnalysis.Buttons.viewMatchingHaplotypes(dataRegionName)</onClick>
</item>
<item text="View Coverage">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'sequence_coverage'})</onClick>
</item>
</item>
<item text="NT SNP Reports">
<item text="NT Mutation Summary, By Position and Base">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'nt_snps_by_pos'})</onClick>
</item>
</item>
<item text="AA SNP Reports">
<item text="AA Mutation Summary, By Position and Codon">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'aa_snps_by_codon'})</onClick>
</item>
<item text="Predicted Drug Resistance Mutations">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'drug_resistance_snps'})</onClick>
</item>
<item text="Quasispecies Viewer">
<onClick>SequenceAnalysis.Buttons.viewSNPs(dataRegionName)</onClick>
</item>
</item>
</item>
</buttonBarOptions>
</table>
<table tableName="ref_aa_features" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.ldk.query.BuiltInColumnsCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Reference AA Features</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&query.queryName=Ref_AA_Features&keyField=rowid&key=${rowid}</tableUrl>
<updateUrl>/ldk/manageRecord.view?schemaName=sequenceanalysis&query.queryName=Ref_AA_Features&keyField=rowid&key=${rowid}</updateUrl>
<insertUrl></insertUrl>
<importUrl></importUrl>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
<columnTitle>Row Id</columnTitle>
</column>
<column columnName="ref_nt_id">
<columnTitle>Ref NT Id</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_nt_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="ref_aa_id">
<columnTitle>Ref AA Id</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_aa_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="name">
</column>
<column columnName="category">
<nullable>true</nullable>
<scale>200</scale>
</column>
<column columnName="aa_start">
<columnTitle>AA Start</columnTitle>
</column>
<column columnName="aa_stop">
<columnTitle>AA Stop</columnTitle>
</column>
<column columnName="aa_sequence">
<nullable>true</nullable>
<inputType>textarea</inputType>
<columnTitle>AA Sequence</columnTitle>
</column>
<column columnName="comment">
<nullable>true</nullable>
<inputType>textarea</inputType>
</column>
<column columnName="container">
</column>
<column columnName="createdby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="modifiedby">
<nullable>true</nullable>
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<!--<isHidden>true</isHidden>-->
</column>
</columns>
</table>
<table tableName="ref_nt_features" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.ldk.query.BuiltInColumnsCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Reference NT Features</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&query.queryName=Ref_NT_Features&keyField=rowid&key=${rowid}</tableUrl>
<updateUrl>/ldk/manageRecord.view?schemaName=sequenceanalysis&query.queryName=Ref_NT_Features&keyField=rowid&key=${rowid}</updateUrl>
<insertUrl></insertUrl>
<importUrl></importUrl>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
</column>
<column columnName="ref_nt_id">
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_nt_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="name">
</column>
<column columnName="category">
<nullable>true</nullable>
<scale>200</scale>
</column>
<column columnName="nt_start">
<columnTitle>NT Start</columnTitle>
</column>
<column columnName="nt_stop">
<columnTitle>NT Stop</columnTitle>
</column>
<column columnName="nt_sequence">
<nullable>true</nullable>
<columnTitle>NT Sequence</columnTitle>
<inputType>textarea</inputType>
</column>
<column columnName="comment">
<nullable>true</nullable>
<inputType>textarea</inputType>
</column>
<column columnName="container">
</column>
<column columnName="createdby">
<nullable>true</nullable>
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
</columns>
</table>
<table tableName="ref_nt_sequences" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.sequenceanalysis.query.SequenceAnalysisCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Reference NT Sequences</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&query.queryName=Ref_NT_Sequences&keyField=rowid&key=${rowid}</tableUrl>
<insertUrl></insertUrl>
<importUrl></importUrl>
<deleteUrl></deleteUrl>
<updateUrl></updateUrl>
<titleColumn>name</titleColumn>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<columnTitle>NT Sequence Id</columnTitle>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
</column>
<column columnName="name">
<nullable>false</nullable>
<scale>220</scale>
<displayWidth>100</displayWidth>
</column>
<column columnName="category">
<nullable>true</nullable>
</column>
<column columnName="subset">
<nullable>true</nullable>
</column>
<column columnName="locus">
<nullable>true</nullable>
</column>
<column columnName="lineage">
<nullable>true</nullable>
</column>
<column columnName="mol_type">
<nullable>true</nullable>
<columnTitle>Molecule Type</columnTitle>
<fk>
<fkDbSchema>laboratory</fkDbSchema>
<fkTable>dna_mol_type</fkTable>
<fkColumnName>mol_type</fkColumnName>
</fk>
</column>
<column columnName="genbank">
<nullable>true</nullable>
<columnTitle>Genbank Id</columnTitle>
<displayColumnFactory>
<className>org.labkey.sequenceanalysis.query.GenbankDisplayColumnFactory</className>
</displayColumnFactory>
</column>
<column columnName="refSeqId">
<nullable>true</nullable>
<columnTitle>RefSeq Id</columnTitle>
<displayColumnFactory>
<className>org.labkey.sequenceanalysis.query.GenbankDisplayColumnFactory</className>
</displayColumnFactory>
</column>
<column columnName="ipd_accession">
<nullable>true</nullable>
<columnTitle>IPD Accession</columnTitle>
<displayColumnFactory>
<className>org.labkey.sequenceanalysis.query.IPDDisplayColumnFactory</className>
</displayColumnFactory>
</column>
<column columnName="species">
<nullable>true</nullable>
<fk>
<fkDbSchema>laboratory</fkDbSchema>
<fkTable>species</fkTable>
<fkColumnName>common_name</fkColumnName>
<fkDisplayColumnName useRawValue="true"/>
</fk>
</column>
<column columnName="geographic_origin">
<nullable>true</nullable>
<scale>200</scale>
</column>
<column columnName="aliases">
<nullable>true</nullable>
<scale>200</scale>
</column>
<column columnName="comments">
<nullable>true</nullable>
<inputType>textarea</inputType>
</column>
<column columnName="seqLength">
<columnTitle>NT Length</columnTitle>
</column>
<column columnName="sequenceFile">
<nullable>true</nullable>
<columnTitle>Sequence File</columnTitle>
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<fk>
<fkDbSchema>exp</fkDbSchema>
<fkTable>data</fkTable>
<fkColumnName>RowId</fkColumnName>
</fk>
</column>
<column columnName="jobid">
<isUserEditable>false</isUserEditable>
<isUnselectable>false</isUnselectable>
<columnTitle>Job Id</columnTitle>
<fk>
<fkDbSchema>pipeline</fkDbSchema>
<fkTable>Job</fkTable>
<fkColumnName>RowId</fkColumnName>
<fkDisplayColumnName>RowId</fkDisplayColumnName>
</fk>
</column>
<column columnName="datedisabled">
<columnTitle>Date Disabled</columnTitle>
<nullable>true</nullable>
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="disabledby">
<columnTitle>Disabled By</columnTitle>
<nullable>true</nullable>
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="downloadSequence" wrappedColumnName="rowid">
<columnTitle>Download Sequence</columnTitle>
<shownInDetailsView>true</shownInDetailsView>
<displayColumnFactory>
<className>org.labkey.sequenceanalysis.query.DownloadSequenceDisplayColumnFactory</className>
</displayColumnFactory>
</column>
<column columnName="container">
</column>
<column columnName="createdby">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<isHidden>true</isHidden>
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
</columns>
<buttonBarOptions includeStandardButtons="true">
<includeScript>laboratory.context</includeScript>
<includeScript>sequenceanalysis/sequenceAnalysis</includeScript>
<includeScript>SequenceAnalysis/window/CreateReferenceLibraryWindow.js</includeScript>
<includeScript>SequenceAnalysis/panel/ImportSequencesFromFastaPanel.js</includeScript>
<includeScript>SequenceAnalysis/window/ImportSequencesFromFastaWindow.js</includeScript>
<includeScript>SequenceAnalysis/window/DownloadSequencesWindow.js</includeScript>
<includeScript>SequenceAnalysis/window/CompareSequencesWindow.js</includeScript>
<includeScript>SequenceAnalysis/window/ConcatenatedSequenceWindow.js</includeScript>
<includeScript>SequenceAnalysis/window/MarkDisabledWindow.js</includeScript>
<item text="Grid Views">
<originalText>Grid Views</originalText>
</item>
<!--<item hidden="true">-->
<!--<originalText>Delete</originalText>-->
<!--</item>-->
<item hidden="true">
<originalText>Charts</originalText>
</item>
<item text="Delete" permission="DELETE" requiresSelection="true" insertBefore="Export" iconCls="trash">
<onClick>SequenceAnalysis.Buttons.deleteTable(dataRegionName);</onClick>
</item>
<item insertPosition="end" text="More Actions" iconCls="ellipsis-h">
<item text="Create Reference Genome">
<onClick>SequenceAnalysis.window.CreateReferenceLibraryWindow.buttonHandler(dataRegionName)</onClick>
</item>
<item text="Import From FASTA">
<onClick>SequenceAnalysis.window.ImportSequencesFromFastaWindow.buttonHandler(dataRegionName)</onClick>
</item>
<item text="Download As FASTA">
<onClick>SequenceAnalysis.window.DownloadSequencesWindow.buttonHandler(dataRegionName)</onClick>
</item>
<item text="Compare FASTA Against Database">
<onClick>SequenceAnalysis.window.CompareSequencesWindow.buttonHandler(dataRegionName)</onClick>
</item>
<item text="Mark Disabled">
<onClick>SequenceAnalysis.window.MarkDisabledWindow.buttonHandler(dataRegionName)</onClick>
</item>
<item text="Create Concatenated Sequence">
<onClick>SequenceAnalysis.window.ConcatenatedSequenceWindow.buttonHandler(dataRegionName)</onClick>
</item>
</item>
</buttonBarOptions>
</table>
<table tableName="drug_resistance" tableDbType="TABLE" useColumnOrder="true">
<auditLogging>DETAILED</auditLogging>
<tableTitle>Drug Resistance Mutations</tableTitle>
<pkColumnName>rowid</pkColumnName>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<isUserEditable>false</isUserEditable>
</column>
<column columnName="ref_nt_id">
<columnTitle>Ref NT Id</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_nt_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="ref_aa_id">
<columnTitle>Ref AA Id</columnTitle>
<fk>
<fkDbSchema>sequenceanalysis</fkDbSchema>
<fkTable>ref_aa_sequences</fkTable>
<fkColumnName>rowid</fkColumnName>
</fk>
</column>
<column columnName="class">
<nullable>true</nullable>
</column>
<column columnName="aa_position">
<columnTitle>AA Position</columnTitle>
</column>
<column columnName="aa_insert_index">
<columnTitle>AA Index</columnTitle>
</column>
<column columnName="reference_aa">
<columnTitle>Reference AA</columnTitle>
<scale>2</scale>
</column>
<column columnName="mutant_aa">
<columnTitle>Mutant AA</columnTitle>
<scale>2</scale>
</column>
<column columnName="drug">
</column>
<column columnName="createdby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="created">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
<column columnName="modifiedby">
<!--<isHidden>true</isHidden>-->
</column>
<column columnName="modified">
<isUserEditable>false</isUserEditable>
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
<nullable>true</nullable>
<scale>29</scale>
<isHidden>true</isHidden>
</column>
</columns>
</table>
<table tableName="analysis_types" tableDbType="TABLE">
<auditLogging>DETAILED</auditLogging>
<tableTitle>Analysis Types</tableTitle>
<pkColumnName>type</pkColumnName>
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<columns>
<column columnName="type">
</column>
</columns>
</table>
<table tableName="sequence_readsets" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
<auditLogging>DETAILED</auditLogging>
<tableTitle>Sequence Readsets</tableTitle>
<pkColumnName>rowid</pkColumnName>
<tableUrl>/sequenceanalysis/readsetDetails.view?id=${rowid}</tableUrl>