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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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15
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22
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23 -----
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24
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25 **What it does**
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26
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27 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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28 The tool will output the input file if it is valid.
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29
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30 -----
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31
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15
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32 **Columns**
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33
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34 date_entered_db
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35 user_specimen_id
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36 field_call
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37 bcoral_genet_id
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38 bsym_genet_id
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39 reef
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40 region
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41 latitude
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42 longitude
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43 geographic_origin
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44 sample_location
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45 latitude_outplant
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46 longitude_outplant
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47 depth
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48 dist_shore
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49 disease_resist
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50 bleach_resist
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51 mortality
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52 tle
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53 spawning
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54 collector_last_name
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55 collector_first_name
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56 org
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57 collection_date
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58 contact_email
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59 seq_facility
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60 array_version
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61 public
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62 public_after_date
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63 </help>
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64 <citations>
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65 </citations>
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66 </tool>
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