Mercurial > repos > devteam > picard
comparison picard_CollectAlignmentSummaryMetrics.xml @ 20:2a17c789e0a5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
| author | iuc |
|---|---|
| date | Tue, 19 Jun 2018 11:28:49 -0400 |
| parents | 5053a18d9bc8 |
| children | 585027e65f3b |
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| 19:5053a18d9bc8 | 20:2a17c789e0a5 |
|---|---|
| 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 2 <description>writes a file containing summary alignment metrics</description> | 2 <description>writes a file containing summary alignment metrics</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>picard_macros.xml</import> | 4 <import>picard_macros.xml</import> |
| 5 <token name="@WRAPPER_VERSION@">0</token> | 5 <token name="@WRAPPER_VERSION@">1</token> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 @java_options@ | 9 @java_options@ |
| 10 @symlink_element_identifier@ | 10 @symlink_element_identifier@ |
| 32 ASSUME_SORTED="${assume_sorted}" | 32 ASSUME_SORTED="${assume_sorted}" |
| 33 | 33 |
| 34 VALIDATION_STRINGENCY="${validation_stringency}" | 34 VALIDATION_STRINGENCY="${validation_stringency}" |
| 35 QUIET=true | 35 QUIET=true |
| 36 VERBOSITY=ERROR | 36 VERBOSITY=ERROR |
| 37 @TMPDIR_OPTION@ | |
| 37 | 38 |
| 38 ]]></command> | 39 ]]></command> |
| 39 <inputs> | 40 <inputs> |
| 40 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> | 41 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> |
| 41 <conditional name="reference_source"> | 42 <conditional name="reference_source"> |