Mercurial > repos > devteam > picard
comparison picard_MergeSamFiles.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 | f9242e01365a |
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| 19:5053a18d9bc8 | 20:2a17c789e0a5 |
|---|---|
| 1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 2 <description>merges multiple SAM/BAM datasets into one</description> | 2 <description>merges multiple SAM/BAM datasets into one</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 picard | 10 picard |
| 25 USE_THREADING=true | 25 USE_THREADING=true |
| 26 SORT_ORDER=coordinate | 26 SORT_ORDER=coordinate |
| 27 VALIDATION_STRINGENCY="${validation_stringency}" | 27 VALIDATION_STRINGENCY="${validation_stringency}" |
| 28 QUIET=true | 28 QUIET=true |
| 29 VERBOSITY=ERROR | 29 VERBOSITY=ERROR |
| 30 @TMPDIR_OPTION@ | |
| 30 | 31 |
| 31 ]]></command> | 32 ]]></command> |
| 32 <inputs> | 33 <inputs> |
| 33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | 34 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
| 34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> | 35 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> |