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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="csv" label="Affymetrix 96 well plate metadata file">
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10
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9 <validator type="expression" message="96 well plate data must have 29 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==29 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="csv"/>
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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.csv" ftype="csv"/>
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18 <output name="output" file="affy_metadata.csv" ftype="csv"/>
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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 29 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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16
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31 * date_entered_db
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32 * user_specimen_id
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33 * field_call
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34 * bcoral_genet_id
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35 * bsym_genet_id
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36 * reef
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37 * region
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38 * latitude
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39 * longitude
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40 * geographic_origin
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41 * sample_location
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42 * latitude_outplant
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43 * longitude_outplant
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44 * depth
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45 * dist_shore
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46 * disease_resist
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47 * bleach_resist
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48 * mortality
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49 * tle
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50 * spawning
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51 * collector_last_name
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52 * collector_first_name
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53 * org
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54 * collection_date
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55 * contact_email
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56 * seq_facility
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57 * array_version
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58 * public
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59 * public_after_date
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60 </help>
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61 <citations>
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62 </citations>
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63 </tool>
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