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comparison picard_SortSam.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool id="picard_SortSam" name="SortSam" version="1.126.0">
2
3 <description>sort SAM/BAM dataset</description>
4
5 <requirements>
6 <requirement type="package" version="1.126.0">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/picard.jar
16 SortSam
17 INPUT="${inputFile}"
18 OUTPUT="${outFile}"
19 SORT_ORDER="${sort_order}"
20 QUIET=true
21 VERBOSITY=ERROR
22 VALIDATION_STRINGENCY=${validation_stringency}
23 </command>
24
25 <inputs>
26 <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"/>
27 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
28 <option value="coordinate" selected="True">Coordinate</option>
29 <option value="queryname">Queryname</option>
30 <option value="unsorted">Unsorted</option>
31 </param>
32 <expand macro="VS" />
33 </inputs>
34
35 <outputs>
36 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
37 </data>
38 </outputs>
39
40 <stdio>
41 <exit_code range="1:" level="fatal"/>
42 </stdio>
43
44 <tests>
45 <test>
46 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
47 <param name="sort_order" value="queryname"/>
48 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
49 </test>
50 </tests>
51
52 <help>
53
54 .. class:: infomark
55
56 **Purpose**
57
58 Sorts the input SAM or BAM.
59
60 @dataset_collections@
61
62 @description@
63
64 SORT_ORDER=SortOrder
65 SO=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
66
67 @more_info@
68
69 </help>
70 </tool>