Mercurial > repos > devteam > picard
comparison picard_BedToIntervalList.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="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 2 <description>convert coordinate data into picard interval list format</description> | 2 <description>convert coordinate data into picard interval list format</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@ |
| 16 #if str( $reference_source.reference_source_selector ) == "history": | 16 #if str( $reference_source.reference_source_selector ) == "history": |
| 17 | 17 |
| 18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" | 18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
| 19 QUIET=true | 19 QUIET=true |
| 20 VERBOSITY=ERROR | 20 VERBOSITY=ERROR |
| 21 @TMPDIR_OPTION@ | |
| 21 | 22 |
| 22 && | 23 && |
| 23 | 24 |
| 24 #else: | 25 #else: |
| 25 | 26 |
| 34 OUTPUT="${outFile}" | 35 OUTPUT="${outFile}" |
| 35 | 36 |
| 36 SEQUENCE_DICTIONARY="${picard_dict}" | 37 SEQUENCE_DICTIONARY="${picard_dict}" |
| 37 QUIET=true | 38 QUIET=true |
| 38 VERBOSITY=ERROR | 39 VERBOSITY=ERROR |
| 40 @TMPDIR_OPTION@ | |
| 39 | 41 |
| 40 ]]></command> | 42 ]]></command> |
| 41 | 43 |
| 42 <inputs> | 44 <inputs> |
| 43 | 45 |