Mercurial > repos > devteam > picard
comparison picard_FastqToSam.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 | 881d7645d1bf |
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| 19:5053a18d9bc8 | 20:2a17c789e0a5 |
|---|---|
| 1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 2 <description>convert Fastq data into unaligned BAM</description> | 2 <description>convert Fastq data into unaligned BAM</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 |
| 64 | 64 |
| 65 SORT_ORDER=coordinate | 65 SORT_ORDER=coordinate |
| 66 VALIDATION_STRINGENCY="${validation_stringency}" | 66 VALIDATION_STRINGENCY="${validation_stringency}" |
| 67 QUIET=true | 67 QUIET=true |
| 68 VERBOSITY=ERROR | 68 VERBOSITY=ERROR |
| 69 | 69 @TMPDIR_OPTION@ |
| 70 ]]></command> | 70 ]]></command> |
| 71 <inputs> | 71 <inputs> |
| 72 <conditional name="input_type"> | 72 <conditional name="input_type"> |
| 73 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> | 73 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> |
| 74 <option value="se">Single end (single dataset)</option> | 74 <option value="se">Single end (single dataset)</option> |