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comparison export_all_sample_data.xml @ 0:f15e63d204b1 draft

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author greg
date Mon, 23 Sep 2019 14:12:31 -0400
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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>
68 <citation type="bibtex">
69 @misc{None,
70 journal = {None},
71 author = {Baums I},
72 title = {Manuscript in preparation},
73 year = {None},
74 url = {http://baumslab.org}
75 </citation>
76 </citations>
77 </tool>
78