source: extensions/net.sf.basedb.reggie/trunk/META-INF/plugin-configurations.xml @ 2021

Last change on this file since 2021 was 2021, checked in by Nicklas Nordborg, 8 years ago

References #499: Export sample sheet for flow cell

First implementation of an export plug-in. It is yet a bit uncertain were some information should be coming from. Eg. the ReadString? is now configuration parameter for the plug-in, but it may be better to store this as an annotation on the flow cell (as is done for 'operator' and 'flow cell id'). Some information is still hard-coded in the plug-in (eg. concentration = 12pM).

File size: 8.2 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
3  <configuration pluginClassName="net.sf.basedb.reggie.plugins.CaliperRunParametersExporter">
4    <configname>High sensitivity</configname>
5    <description />
6    <parameter>
7      <name>DataPath</name>
8      <label>Data Path</label>
9      <description>Enter the path on the Caliper computer where data files should be saved.If not specified, the descision is left to the Caliper software.</description>
10      <class>java.lang.String</class>
11      <value>C:\CaliperFiles</value>
12    </parameter>
13    <parameter>
14      <name>sensitivity</name>
15      <label>Sensitivity</label>
16      <description>This parameter decide which RNA QC aliquots from the plate are selected for a specific run:
17Standard = extracts with QCHiSense=FALSE or missing are selected
18High = extracts with QCHiSense=TRUE are selected</description>
19      <class>java.lang.String</class>
20      <value>High</value>
21    </parameter>
22    <parameter>
23      <name>PlateName</name>
24      <label>Plate Name</label>
25      <description>Enter the name of the plate as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
26      <class>java.lang.String</class>
27      <value>FrameStar Skirted 96 [sip 2mm]</value>
28    </parameter>
29    <parameter>
30      <name>AssayType</name>
31      <label>Assay Type</label>
32      <description>Enter the name of the Assay Type parameter as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
33      <class>java.lang.String</class>
34      <value>HT RNA High Sens</value>
35    </parameter>
36  </configuration>
37  <configuration pluginClassName="net.sf.basedb.reggie.plugins.CaliperRunParametersExporter">
38    <configname>Standard sensitivity</configname>
39    <description />
40    <parameter>
41      <name>DataPath</name>
42      <label>Data Path</label>
43      <description>Enter the path on the Caliper computer where data files should be saved.If not specified, the descision is left to the Caliper software.</description>
44      <class>java.lang.String</class>
45      <value>C:\CaliperFiles</value>
46    </parameter>
47    <parameter>
48      <name>sensitivity</name>
49      <label>Sensitivity</label>
50      <description>This parameter decide which RNA QC aliquots from the plate are selected for a specific run:
51Standard = extracts without the QCHiSense annotation are selected
52High = extracts with QCHiSense=TRUE are selected</description>
53      <class>java.lang.String</class>
54      <value>Standard</value>
55    </parameter>
56    <parameter>
57      <name>PlateName</name>
58      <label>Plate Name</label>
59      <description>Enter the name of the plate as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
60      <class>java.lang.String</class>
61      <value>FrameStar Skirted 96 [sip 2mm]</value>
62    </parameter>
63    <parameter>
64      <name>AssayType</name>
65      <label>Assay Type</label>
66      <description>Enter the name of the Assay Type paramter as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
67      <class>java.lang.String</class>
68      <value>HT RNA Std Sens</value>
69    </parameter>
70  </configuration>
71  <configuration pluginClassName="net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter">
72    <configname>HT DNA 1K Ver2 (96)</configname>
73    <description />
74    <parameter>
75      <name>DataPath</name>
76      <label>Data Path</label>
77      <description>Enter the path on the Caliper computer where data files should be saved.If not specified, the descision is left to the Caliper software.</description>
78      <class>java.lang.String</class>
79      <value>C:\CaliperLibFiles</value>
80    </parameter>
81    <parameter>
82      <name>PlateName</name>
83      <label>Plate Name</label>
84      <description>Enter the name of the plate as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
85      <class>java.lang.String</class>
86      <value>FrameStar Skirted 96 [sip 2mm]</value>
87    </parameter>
88    <parameter>
89      <name>AssayType</name>
90      <label>Assay Type</label>
91      <description>Enter the name of the Assay Type parameter as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
92      <class>java.lang.String</class>
93      <value>HT DNA 1K Ver2</value>
94    </parameter>
95  </configuration>
96  <configuration pluginClassName="net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter">
97    <configname>HT DNA 1K Ver2 (384)</configname>
98    <description />
99    <parameter>
100      <name>DataPath</name>
101      <label>Data Path</label>
102      <description>Enter the path on the Caliper computer where data files should be saved.If not specified, the descision is left to the Caliper software.</description>
103      <class>java.lang.String</class>
104      <value>C:\CaliperLibFiles</value>
105    </parameter>
106    <parameter>
107      <name>PlateName</name>
108      <label>Plate Name</label>
109      <description>Enter the name of the plate as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
110      <class>java.lang.String</class>
111      <value>BioRad Hard-shell 384</value>
112    </parameter>
113    <parameter>
114      <name>AssayType</name>
115      <label>Assay Type</label>
116      <description>Enter the name of the Assay Type parameter as it appears in the Run dialog in the Caliper software. If an incorrect name is used the exported file can't be used by Caliper.</description>
117      <class>java.lang.String</class>
118      <value>HT DNA 1K Ver2</value>
119    </parameter>
120    <parameter>
121      <name>RemapTo384</name>
122      <label>Uses 384-well plate</label>
123      <description>Enable this option if the extracts are placed on a 384-well plate. The coordinates are mapped so that every other row/colum is used. Eg. A1, A3 A5..., C1, C3, etc.</description>
124      <class>java.lang.Boolean</class>
125      <value>true</value>
126    </parameter>
127  </configuration>
128  <configuration pluginClassName="net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter">
129    <configname>SCAN-B 2x50</configname>
130    <description>Configuration for the default SCAN-B setup. Read string is Y54N1I6J1Y53N1.</description>
131    <parameter>
132      <name>SequencingCenter</name>
133      <label>Sequencing center</label>
134      <description>LuOnk</description>
135      <class>java.lang.String</class>
136      <value>LuBMC</value>
137    </parameter>
138    <parameter>
139      <name>ReadString</name>
140      <label>Read string</label>
141      <description>Pattern describing how each sequencing cycle is used.
142
143Y = the cycle should be used as part of an insert read
144N = the cycle should be skipped
145I = the cycle should be used as part of the index (barcode)
146J = the cycle is part of the index but should not be used in demultiplexing
147
148A number means repeat the preceding letter this many times.
149
150The person responsible for the library should enter the requested pattern of sequencing cycles here. Checked and corrected by the operator who loads the libraries on the flowcell.</description>
151      <class>java.lang.String</class>
152      <value>Y54N1I6J1Y53N1</value>
153    </parameter>
154    <parameter>
155      <name>Project</name>
156      <label>Project</label>
157      <description>Project name. Lower case letters (a-z), numbers and underscore are permitted. After sequencing is done, the sequence reads are converted to bam format and demultiplexed. One bam file is produced per lane and index. The bam files are deposited in separate folders for each project.</description>
158      <class>java.lang.String</class>
159      <value>scanb</value>
160    </parameter>
161    <parameter>
162      <name>Width</name>
163      <label>Width</label>
164      <description>The width of the library size distribution at approximately 2/3 peak height.</description>
165      <class>java.lang.Integer</class>
166      <value>100</value>
167    </parameter>
168  </configuration>
169</configfile>
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