Mercurial > repos > devteam > picard
comparison picard_FilterSamReads.xml @ 32:f9242e01365a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
| author | iuc |
|---|---|
| date | Mon, 25 Sep 2023 08:32:17 +0000 |
| parents | 2a17c789e0a5 |
| children | 3f254c5ced1d |
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| 31:585027e65f3b | 32:f9242e01365a |
|---|---|
| 16 OUTPUT=query_sorted_bam.bam | 16 OUTPUT=query_sorted_bam.bam |
| 17 SORT_ORDER=queryname | 17 SORT_ORDER=queryname |
| 18 VALIDATION_STRINGENCY=LENIENT | 18 VALIDATION_STRINGENCY=LENIENT |
| 19 QUIET=true | 19 QUIET=true |
| 20 VERBOSITY=ERROR | 20 VERBOSITY=ERROR |
| 21 @TMPDIR_OPTION@ | |
| 22 | 21 |
| 23 && | 22 && |
| 24 | 23 |
| 25 picard | 24 picard |
| 26 FilterSamReads | 25 FilterSamReads |
| 34 OUTPUT="${outFile}" | 33 OUTPUT="${outFile}" |
| 35 SORT_ORDER=coordinate | 34 SORT_ORDER=coordinate |
| 36 VALIDATION_STRINGENCY="${validation_stringency}" | 35 VALIDATION_STRINGENCY="${validation_stringency}" |
| 37 QUIET=true | 36 QUIET=true |
| 38 VERBOSITY=ERROR | 37 VERBOSITY=ERROR |
| 39 @TMPDIR_OPTION@ | |
| 40 | 38 |
| 41 ]]></command> | 39 ]]></command> |
| 42 <inputs> | 40 <inputs> |
| 43 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | 41 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
| 44 <conditional name="filter_type"> | 42 <conditional name="filter_type"> |