Mercurial > repos > devteam > picard
comparison picard_FilterSamReads.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 3d4f1fa26f0e |
| children | 05087b27692a |
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| 7:379fdf4c41ac | 8:3a3234d7a2e8 |
|---|---|
| 1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0"> | 1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0"> |
| 2 <description>include or exclude aligned and unaligned reads and read lists</description> | 2 <description>include or exclude aligned and unaligned reads and read lists</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.126.0">picard</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <macros> | 3 <macros> |
| 8 <import>picard_macros.xml</import> | 4 <import>picard_macros.xml</import> |
| 9 </macros> | 5 </macros> |
| 10 | 6 <expand macro="requirements" /> |
| 11 <command> | 7 <command> |
| 12 @java_options@ | 8 @java_options@ |
| 13 | 9 |
| 14 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order | 10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order |
| 15 | 11 |
| 39 QUIET=true | 35 QUIET=true |
| 40 VERBOSITY=ERROR | 36 VERBOSITY=ERROR |
| 41 | 37 |
| 42 </command> | 38 </command> |
| 43 <inputs> | 39 <inputs> |
| 44 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | 40 <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"/> |
| 45 <conditional name="filter_type"> | 41 <conditional name="filter_type"> |
| 46 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> | 42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> |
| 47 <option value="includeAligned">Include aligned</option> | 43 <option value="includeAligned">Include aligned</option> |
| 48 <option value="excludeAligned">Exclude aligned</option> | 44 <option value="excludeAligned">Exclude aligned</option> |
| 49 <option value="includeReadList">Include read list</option> | 45 <option value="includeReadList">Include read list</option> |