DiscvrLabKeyModules/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml at e44814298f735503a0d169ae190b9698170f6cd1 · LabKey/DiscvrLabKeyModules · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
<query xmlns="http://labkey.org/data/xml/query">
    <metadata>
        <tables xmlns="http://labkey.org/data/xml">
            <table tableName="alignment_summary_grouped" tableDbType="TABLE">
                <javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
                <tableTitle>Alignment Summary</tableTitle>
                <pkColumnName>rowids</pkColumnName>
                <columns>
                    <column columnName="analysis_id">
                        <columnTitle>Analysis Id</columnTitle>
                        <fk>
                            <fkDbSchema>sequenceanalysis</fkDbSchema>
                            <fkTable>sequence_analyses</fkTable>
                            <fkColumnName>rowid</fkColumnName>
                        </fk>
                    </column>
                    <column columnName="rowids">
                        <columnTitle>RowIds</columnTitle>
                        <isHidden>true</isHidden>
                        <isKeyField>true</isKeyField>
                    </column>
                    <column columnName="alleles">
                        <displayWidth>200</displayWidth>
                    </column>
                    <column columnName="lineages">
                        <displayWidth>150</displayWidth>
                    </column>
                    <column columnName="total_forward">
                        <columnTitle>Total First-Mate Reads</columnTitle>
                        <description>The column shows the number of alignments that contain a first-mate or singleton read</description>
                    </column>
                    <column columnName="total_reverse">
                        <columnTitle>Total Second-Mate Reads</columnTitle>
                        <description>The column shows the number of alignments that contain a second-mate read</description>
                    </column>
                    <column columnName="valid_pairs">
                        <columnTitle>Total Valid Pairs</columnTitle>
                        <description>The column shows the number of alignments that contain valid paired reads (both forward and reverse)</description>
                    </column>
                    <column columnName="percent_from_locus">
                        <conditionalFormats>
                            <conditionalFormat>
                                <filters>
                                    <filter operator="lte" value="1.0"/>
                                </filters>
                                <backgroundColor>FF6666</backgroundColor>
                            </conditionalFormat>
                            <conditionalFormat>
                                <filters>
                                    <filter operator="gt" value="1.0"/>
                                    <filter operator="lt" value="7.0"/>
                                </filters>
                                <backgroundColor>FFFF00</backgroundColor>
                            </conditionalFormat>
                            <conditionalFormat>
                                <filters>
                                    <filter operator="gte" value="7.0"/>
                                </filters>
                                <backgroundColor>00CC33</backgroundColor>
                            </conditionalFormat>
                        </conditionalFormats>
                    </column>
                    <column columnName="nAlignments">
                        <columnTitle># Alignments</columnTitle>
                        <isHidden>true</isHidden>
                    </column>
                    <column columnName="nLoci">
                        <columnTitle># Loci</columnTitle>
                        <isHidden>true</isHidden>
                    </column>
                </columns>
            </table>
        </tables>
    </metadata>
</query>