Mercurial > repos > greg > ensure_synced
comparison ensure_synced.xml @ 0:9180906544b6 draft
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| author | greg |
|---|---|
| date | Thu, 15 Aug 2019 10:37:49 -0400 |
| parents | |
| children | 281f38df3c58 |
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| -1:000000000000 | 0:9180906544b6 |
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| 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 |