|
5
|
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> |
