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1 <tool id="export_all_sample_data" name="Export all sample data" version="1.0.0">
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2 <description>from the stag database</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 python '$__tool_directory__/export_all_sample_data.py'
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5 --database_connection_string '$__app__.config.corals_database_connection'
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6 --output '$output']]></command>
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7 <inputs>
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="tabular" label="${tool.name}"/>
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11 </outputs>
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12 <tests>
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13 <test>
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14 <!--Testing this tool is a bit difficult at the current time.-->
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15 </test>
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16 </tests>
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17 <help>
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18 **What it does**
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19
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20 Generates a tabular dataset of all samples and associated metadata in the stag database.
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21
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22 -----
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23
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24 **Output Columns**
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25
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26 * Affymetrix ID
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27 * Sample ID
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28 * User Specimen ID
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29 * Field Call
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30 * Sample Depth
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31 * Percent Missing Data Coral
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32 * Percent Heterozygous Coral
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33 * Percent Acerv Coral
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34 * Percent Apalm Coral
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35 * Bcoral Genet ID
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36 * Registry ID
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37 * DNA Extraction Method
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38 * DNA Concentration
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39 * Colony Location
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40 * Colony Latitude
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41 * Colony Longitude
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42 * Colony Depth
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43 * Reef Name
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44 * Region
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45 * Reef Latitude
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46 * Reef Longitude
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47 * GPS Coordinates Associated With
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48 * Coral MLG Clonal ID
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49 * Coral MLG Rep Sample ID
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50 * Genetic Coral Species Call
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51 * Spawning
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52 * Sperm Motility
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53 * TLE
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54 * Disease Resist
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55 * Bleach Resist
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56 * Mortality
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57 * Healing Time
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58 * Sequencing Facility
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59 * Array Version
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60 * Plate Barcode
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61 * Collector Last Name
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62 * First Name
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63 * Organization
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64 * Email
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65 * Collection Date
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66 </help>
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67 <citations>
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68 <citation type="bibtex">
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69 @misc{None,
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70 journal = {None},
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71 author = {Baums I},
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72 title = {Manuscript in preparation},
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73 year = {None},
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74 url = {http://baumslab.org}
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75 </citation>
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76 </citations>
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77 </tool>
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78
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