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0
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1 <tool id="ensure_synced" name="Ensure synchronized" version="1.0.0">
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2 <description>analysis components</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 #set affy_ids_from_file = 'affy_ids_from_file.txt'
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5 grep "#CHROM" $input > test.head &&
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1
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6 tr '\t' '\n' < test.head > $affy_ids_from_file &&
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7 python '$__tool_directory__/ensure_synced.py'
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8 --database_connection_string '$__app__.config.corals_database_connection'
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9 --affy_ids_from_file '$affy_ids_from_file'
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10 --output '$output']]></command>
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11 <inputs>
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12 <param name="input" format="vcf" type="data" label="All genotyped samples file"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="txt" label="${tool.name} (process log) on ${on_string}"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <!--Testing this tool is a bit difficult at the current time.-->
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20 </test>
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21 </tests>
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22 <help>
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23 **What it does**
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24
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25 Compares the set of Affymetrix id strings contained within a selected VCF file with the set of Affymetrix ids contained
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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
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27 sets are equivalent, the file and the database are considered to be in sync with each other.
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28 </help>
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29 <citations>
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5
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30 <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation>
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0
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31 </citations>
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32 </tool>
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33
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