Mercurial > repos > devteam > picard
comparison picard_SortSam.xml @ 8:e417b1d6288d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
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date | Tue, 06 Dec 2016 10:04:26 -0500 |
parents | 08f69add4d06 |
children | 41b8d087a2d2 |
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7:08f69add4d06 | 8:e417b1d6288d |
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10 ln -s '${outFile}' output.sam && | 10 ln -s '${outFile}' output.sam && |
11 #else: | 11 #else: |
12 #set $output = $outFile | 12 #set $output = $outFile |
13 #end if | 13 #end if |
14 @java_options@ | 14 @java_options@ |
15 @symlink_element_identifier@ | |
15 picard | 16 picard |
16 SortSam | 17 SortSam |
17 INPUT="${inputFile}" | 18 INPUT='$inputFile.element_identifier' |
18 OUTPUT='${output}' | 19 OUTPUT='${output}' |
19 SORT_ORDER="${sort_order}" | 20 SORT_ORDER="${sort_order}" |
20 QUIET=true | 21 QUIET=true |
21 VERBOSITY=ERROR | 22 VERBOSITY=ERROR |
22 VALIDATION_STRINGENCY=${validation_stringency} | 23 VALIDATION_STRINGENCY=${validation_stringency} |