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comparison ensure_synced.xml @ 1:281f38df3c58 draft

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author greg
date Thu, 15 Aug 2019 14:55:20 -0400
parents 9180906544b6
children a7be280fa304
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0:9180906544b6 1:281f38df3c58
1 <tool id="ensure_synced" name="Ensure synchronized" version="1.0.0"> 1 <tool id="ensure_synced" name="Ensure synchronized" version="1.0.0">
2 <description>analysis components</description> 2 <description>analysis components</description>
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 #set affy_ids_from_file = 'affy_ids_from_file.txt' 4 #set affy_ids_from_file = 'affy_ids_from_file.txt'
5 grep "#CHROM" $input > test.head && 5 grep "#CHROM" $input > test.head &&
6 tr '\t' '\n' < test.head > $affy_ids_from_file 6 tr '\t' '\n' < test.head > $affy_ids_from_file &&
7 python '$__tool_directory__/ensure_synced.py' 7 python '$__tool_directory__/ensure_synced.py'
8 --database_connection_string '$__app__.config.corals_database_connection' 8 --database_connection_string '$__app__.config.corals_database_connection'
9 --affy_ids_from_file '$affy_ids_from_file' 9 --affy_ids_from_file '$affy_ids_from_file'
10 --output '$output']]></command> 10 --output '$output']]></command>
11 <inputs> 11 <inputs>