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comparison bamtools-filter.xml @ 7:4fe8a75334c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit c72d58cbe6a99bc8f9fde26fdde45b0c222890df
author iuc
date Fri, 20 Jul 2018 04:14:40 -0400
parents 82658c080fd0
children 1dfd95ee241e
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6:82658c080fd0 7:4fe8a75334c8
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 cp '$script_file' '$out_file2' && 9 cp '$script_file' '$out_file2' &&
10 ln -s '${input_bam}' localbam.bam && 10 ln -s '${input_bam}' localbam.bam &&
11 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai && 11 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
12 cat '$script_file' &&
12 bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1' 13 bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'
13 ]]> 14 ]]>
14 </command> 15 </command>
15 <configfiles> 16 <configfiles>
16 <configfile name="script_file"> 17 <configfile name="script_file">