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1 <tool id="validate_affy_metadata" name="Validate Affymetrix metadata" version="1.0.0">
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2 <description>for 96 well plate</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 python '$__tool_directory__/validate_affy_metadata.py'
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5 --input '$input'
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6 --output '$output']]></command>
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7 <inputs>
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8 <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file">
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9 <validator type="expression" message="96 well plate data must have 32 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==32 and value.metadata.data_lines<=96]]></validator>
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10 </param>
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="tabular"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input" value="affy_metadata.tabular" ftype="tabular"/>
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18 <output name="output" file="affy_metadata.tabular" ftype="tabular"/>
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19 </test>
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20 </tests>
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21 <help>
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22 **What it does**
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23
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24 Validates an Affymetrix metadata file for 96 well plate data. These files consist of 32 columns and no more than 96 data lines.
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25 The tool will output the input file if it is valid.
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26
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27 -----
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28
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29 **Columns**
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30
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31 * user_specimen_id
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32 * field_call
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33 * bcoral_genet_id
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34 * bsym_genet_id
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35 * reef
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36 * region
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37 * latitude
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38 * longitude
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39 * geographic_origin
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40 * colony_location
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41 * depth
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42 * disease_resist
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43 * bleach_resist
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44 * mortality
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45 * tle
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46 * spawning
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47 * collector_last_name
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48 * collector_first_name
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49 * org
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50 * collection_date
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51 * contact_email
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52 * seq_facility
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53 * array_version
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54 * public
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55 * public_after_date
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56 * sperm_motility
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57 * healing_time
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58 * dna_extraction_method
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59 * dna_concentration
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60 * registry_id
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61 * result_folder_name
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62 * plate_barcode
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63 </help>
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64 <citations>
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65 <citation type="bibtex">
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66 @misc{None,
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67 journal = {None},
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68 author = {Baums I},
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69 title = {Manuscript in preparation},
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70 year = {None},
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71 url = {http://baumslab.org}
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72 </citation>
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73 </citations>
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74 </tool>
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75
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