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comparison picard_SortSam.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 f9242e01365a
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equal deleted inserted replaced
19:5053a18d9bc8 20:2a17c789e0a5
1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>sort SAM/BAM dataset</description> 2 <description>sort SAM/BAM dataset</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 #if $sort_order == "queryname": 9 #if $sort_order == "queryname":
10 #set $output = "output.sam" 10 #set $output = "output.sam"
19 INPUT='$escaped_element_identifier' 19 INPUT='$escaped_element_identifier'
20 OUTPUT='${output}' 20 OUTPUT='${output}'
21 SORT_ORDER="${sort_order}" 21 SORT_ORDER="${sort_order}"
22 QUIET=true 22 QUIET=true
23 VERBOSITY=ERROR 23 VERBOSITY=ERROR
24 @TMPDIR_OPTION@
24 VALIDATION_STRINGENCY=${validation_stringency} 25 VALIDATION_STRINGENCY=${validation_stringency}
25 ]]></command> 26 ]]></command>
26 27
27 <inputs> 28 <inputs>
28 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 29 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>