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comparison picard_SamToFastq.xml @ 20:2a17c789e0a5 draft

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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 9ffcddf6f9c0
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19:5053a18d9bc8 20:2a17c789e0a5
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"/>