Mercurial > repos > devteam > picard
comparison picard_SamToFastq.xml @ 15:a5a13ea16d17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
| author | iuc |
|---|---|
| date | Tue, 19 Jun 2018 11:28:30 -0400 |
| parents | 486d7500da69 |
| children | 1181366ba593 |
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| 14:486d7500da69 | 15:a5a13ea16d17 |
|---|---|
| 1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> | 2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</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 | 9 |
| 10 echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below) | 10 echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below) |
| 49 | 49 |
| 50 | 50 |
| 51 VALIDATION_STRINGENCY="${validation_stringency}" | 51 VALIDATION_STRINGENCY="${validation_stringency}" |
| 52 QUIET=true | 52 QUIET=true |
| 53 VERBOSITY=ERROR | 53 VERBOSITY=ERROR |
| 54 @TMPDIR_OPTION@ | |
| 54 | 55 |
| 55 ]]></command> | 56 ]]></command> |
| 56 <inputs> | 57 <inputs> |
| 57 | 58 |
| 58 <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"/> | 59 <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"/> |