|
0
|
1 <tool id="ensure_synced" name="Ensure synchronized" version="1.0.0">
|
|
|
2 <description>analysis components</description>
|
|
|
3 <command detect_errors="exit_code"><![CDATA[
|
|
|
4 #set affy_ids_from_file = 'affy_ids_from_file.txt'
|
|
|
5 grep "#CHROM" $input > test.head &&
|
|
|
6 tr '\t' '\n' < test.head > $affy_ids_from_file
|
|
|
7 python '$__tool_directory__/ensure_synced.py'
|
|
|
8 --database_connection_string '$__app__.config.corals_database_connection'
|
|
|
9 --affy_ids_from_file '$affy_ids_from_file'
|
|
|
10 --output '$output']]></command>
|
|
|
11 <inputs>
|
|
|
12 <param name="input" format="vcf" type="data" label="All genotyped samples file"/>
|
|
|
13 </inputs>
|
|
|
14 <outputs>
|
|
|
15 <data name="output" format="txt" label="${tool.name} (process log) on ${on_string}"/>
|
|
|
16 </outputs>
|
|
|
17 <tests>
|
|
|
18 <test>
|
|
|
19 <!--Testing this tool is a bit difficult at the current time.-->
|
|
|
20 </test>
|
|
|
21 </tests>
|
|
|
22 <help>
|
|
|
23 **What it does**
|
|
|
24
|
|
|
25 Compares the set of Affymetrix id strings contained within a selected VCF file with the set of Affymetrix ids contained
|
|
|
26 in the affy_id column of the sample table in the corals (stag) database for all samples not in a failed state. If these
|
|
|
27 sets are equivalent, the file and the database are considered to be in sync with each other.
|
|
|
28 </help>
|
|
|
29 <citations>
|
|
|
30 <citation type="bibtex">
|
|
|
31 @misc{None,
|
|
|
32 journal = {None},
|
|
|
33 author = {Baums I},
|
|
|
34 title = {Manuscript in preparation},
|
|
|
35 year = {None},
|
|
|
36 url = {http://baumslab.org}
|
|
|
37 </citation>
|
|
|
38 </citations>
|
|
|
39 </tool>
|
|
|
40
|
