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comparison picard_SortSam.xml @ 3:52fdfc45590a 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 15:32:31 -0400
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children 2f3cdd537834
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2:93ace7e49295 3:52fdfc45590a
1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.0">
2 <description>sort SAM/BAM dataset</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9 java -jar \$JAVA_JAR_PATH/picard.jar
10 SortSam
11 INPUT="${inputFile}"
12 OUTPUT="${outFile}"
13 SORT_ORDER="${sort_order}"
14 QUIET=true
15 VERBOSITY=ERROR
16 VALIDATION_STRINGENCY=${validation_stringency}
17 </command>
18
19 <inputs>
20 <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"/>
21 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
22 <option value="coordinate" selected="True">Coordinate</option>
23 <option value="queryname">Queryname</option>
24 <option value="unsorted">Unsorted</option>
25 </param>
26 <expand macro="VS" />
27 </inputs>
28
29 <outputs>
30 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
31 </data>
32 </outputs>
33
34 <stdio>
35 <exit_code range="1:" level="fatal"/>
36 </stdio>
37
38 <tests>
39 <test>
40 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
41 <param name="sort_order" value="queryname"/>
42 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
43 </test>
44 </tests>
45
46 <help>
47
48 .. class:: infomark
49
50 **Purpose**
51
52 Sorts the input SAM or BAM.
53
54 @dataset_collections@
55
56 @description@
57
58 SORT_ORDER=SortOrder
59 SO=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
60
61 @more_info@
62
63 </help>
64 </tool>