|
0
|
1 <tool id="export_all_sample_data" name="Export all sample data" version="1.0.0">
|
|
|
2 <description>from the stag database</description>
|
|
|
3 <command detect_errors="exit_code"><![CDATA[
|
|
|
4 python '$__tool_directory__/export_all_sample_data.py'
|
|
|
5 --database_connection_string '$__app__.config.corals_database_connection'
|
|
|
6 --output '$output']]></command>
|
|
|
7 <inputs>
|
|
|
8 </inputs>
|
|
|
9 <outputs>
|
|
|
10 <data name="output" format="tabular" label="${tool.name}"/>
|
|
|
11 </outputs>
|
|
|
12 <tests>
|
|
|
13 <test>
|
|
|
14 <!--Testing this tool is a bit difficult at the current time.-->
|
|
|
15 </test>
|
|
|
16 </tests>
|
|
|
17 <help>
|
|
|
18 **What it does**
|
|
|
19
|
|
|
20 Generates a tabular dataset of all samples and associated metadata in the stag database.
|
|
|
21
|
|
|
22 -----
|
|
|
23
|
|
|
24 **Output Columns**
|
|
|
25
|
|
|
26 * Affymetrix ID
|
|
|
27 * Sample ID
|
|
|
28 * User Specimen ID
|
|
|
29 * Field Call
|
|
|
30 * Sample Depth
|
|
|
31 * Percent Missing Data Coral
|
|
|
32 * Percent Heterozygous Coral
|
|
|
33 * Percent Acerv Coral
|
|
|
34 * Percent Apalm Coral
|
|
|
35 * Bcoral Genet ID
|
|
|
36 * Registry ID
|
|
|
37 * DNA Extraction Method
|
|
|
38 * DNA Concentration
|
|
|
39 * Colony Location
|
|
|
40 * Colony Latitude
|
|
|
41 * Colony Longitude
|
|
|
42 * Colony Depth
|
|
|
43 * Reef Name
|
|
|
44 * Region
|
|
|
45 * Reef Latitude
|
|
|
46 * Reef Longitude
|
|
|
47 * GPS Coordinates Associated With
|
|
|
48 * Coral MLG Clonal ID
|
|
|
49 * Coral MLG Rep Sample ID
|
|
|
50 * Genetic Coral Species Call
|
|
|
51 * Spawning
|
|
|
52 * Sperm Motility
|
|
|
53 * TLE
|
|
|
54 * Disease Resist
|
|
|
55 * Bleach Resist
|
|
|
56 * Mortality
|
|
|
57 * Healing Time
|
|
|
58 * Sequencing Facility
|
|
|
59 * Array Version
|
|
|
60 * Plate Barcode
|
|
|
61 * Collector Last Name
|
|
|
62 * First Name
|
|
|
63 * Organization
|
|
|
64 * Email
|
|
|
65 * Collection Date
|
|
|
66 </help>
|
|
|
67 <citations>
|
|
3
|
68 <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation>
|
|
0
|
69 </citations>
|
|
|
70 </tool>
|
|
|
71
|
