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comparison validate_affy_metadata.xml @ 0:80d672b3e6dd draft

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author greg
date Thu, 15 Aug 2019 13:17:41 -0400
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1 <tool id="validate_affy_metadata" name="Validate Affymetrix metadata" version="1.0.0">
2 <description>for 96 well plate</description>
3 <command detect_errors="exit_code"><![CDATA[
4 python '$__tool_directory__/validate_affy_metadata.py'
5 --input '$input'
6 --output '$output']]></command>
7 <inputs>
8 <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file">
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>
10 </param>
11 </inputs>
12 <outputs>
13 <data name="output" format="tabular"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="input" value="affy_metadata.tabular" ftype="tabular"/>
18 <output name="output" file="affy_metadata.tabular" ftype="tabular"/>
19 </test>
20 </tests>
21 <help>
22 **What it does**
23
24 Validates an Affymetrix metadata file for 96 well plate data. These files consist of 32 columns and no more than 96 data lines.
25 The tool will output the input file if it is valid.
26
27 -----
28
29 **Columns**
30
31 * user_specimen_id
32 * field_call
33 * bcoral_genet_id
34 * bsym_genet_id
35 * reef
36 * region
37 * latitude
38 * longitude
39 * geographic_origin
40 * colony_location
41 * depth
42 * disease_resist
43 * bleach_resist
44 * mortality
45 * tle
46 * spawning
47 * collector_last_name
48 * collector_first_name
49 * org
50 * collection_date
51 * contact_email
52 * seq_facility
53 * array_version
54 * public
55 * public_after_date
56 * sperm_motility
57 * healing_time
58 * dna_extraction_method
59 * dna_concentration
60 * registry_id
61 * result_folder_name
62 * plate_barcode
63 </help>
64 <citations>
65 <citation type="bibtex">
66 @misc{None,
67 journal = {None},
68 author = {Baums I},
69 title = {Manuscript in preparation},
70 year = {None},
71 url = {http://baumslab.org}
72 </citation>
73 </citations>
74 </tool>
75