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comparison picard_SortSam.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool id="picard_SortSam" name="SortSam" version="1.122.0">
2
3 <description>sort SAM/BAM dataset</description>
4
5 <requirements>
6 <requirement type="package" version="1.122.0">picard</requirement>
7 </requirements>
8
9 <macros>
10 <import>picard_macros.xml</import>
11 </macros>
12
13 <command>
14 @java_options@
15 java -jar \$JAVA_JAR_PATH/SortSam.jar
16 INPUT="${inputFile}"
17 OUTPUT="${outFile}"
18 SORT_ORDER="${sort_order}"
19 QUIET=true
20 VERBOSITY=ERROR
21 VALIDATION_STRINGENCY=${validation_stringency}
22 </command>
23
24 <inputs>
25 <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"/>
26 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
27 <option value="coordinate" selected="True">Coordinate</option>
28 <option value="queryname">Queryname</option>
29 <option value="unsorted">Unsorted</option>
30 </param>
31 <expand macro="VS" />
32 </inputs>
33
34 <outputs>
35 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
36 </data>
37 </outputs>
38
39 <stdio>
40 <exit_code range="1:" level="fatal"/>
41 </stdio>
42
43 <tests>
44 <test>
45 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
46 <param name="sort_order" value="queryname"/>
47 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
48 </test>
49 </tests>
50
51 <help>
52
53 .. class:: infomark
54
55 **Purpose**
56
57 Sorts the input SAM or BAM.
58
59 @dataset_collections@
60
61 @description@
62
63 SORT_ORDER=SortOrder
64 SO=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
65
66 @more_info@
67
68 </help>
69 </tool>