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comparison picard_FilterSamReads.xml @ 8:3a3234d7a2e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 3d4f1fa26f0e
children 05087b27692a
comparison
equal deleted inserted replaced
7:379fdf4c41ac 8:3a3234d7a2e8
1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0"> 1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0">
2 <description>include or exclude aligned and unaligned reads and read lists</description> 2 <description>include or exclude aligned and unaligned reads and read lists</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros> 3 <macros>
8 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
9 </macros> 5 </macros>
10 6 <expand macro="requirements" />
11 <command> 7 <command>
12 @java_options@ 8 @java_options@
13 9
14 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order 10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
15 11
39 QUIET=true 35 QUIET=true
40 VERBOSITY=ERROR 36 VERBOSITY=ERROR
41 37
42 </command> 38 </command>
43 <inputs> 39 <inputs>
44 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 40 <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"/>
45 <conditional name="filter_type"> 41 <conditional name="filter_type">
46 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> 42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
47 <option value="includeAligned">Include aligned</option> 43 <option value="includeAligned">Include aligned</option>
48 <option value="excludeAligned">Exclude aligned</option> 44 <option value="excludeAligned">Exclude aligned</option>
49 <option value="includeReadList">Include read list</option> 45 <option value="includeReadList">Include read list</option>