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comparison picard_CleanSam.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_CleanSam" name="CleanSam" version="1.122.0">
2
3 <description>perform SAM/BAM grooming</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/CleanSam.jar
16 INPUT="${inputFile}"
17 OUTPUT="${outFile}"
18 QUIET=true
19 VERBOSITY=ERROR
20 VALIDATION_STRINGENCY=${validation_stringency}
21 </command>
22
23 <inputs>
24 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
25
26 <expand macro="VS" />
27
28 </inputs>
29
30 <outputs>
31 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
32 </data>
33 </outputs>
34
35 <stdio>
36 <exit_code range="1:" level="fatal"/>
37 </stdio>
38
39 <tests>
40 <test>
41 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
42 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
43 </test>
44 </tests>
45
46 <help>
47
48 .. class:: infomark
49
50 **Purpose**
51
52 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
53
54 1. to soft-clip an alignment that hangs off the end of its reference sequence.
55 2. to set MAPQ to 0 if a read is unmapped.
56
57 @dataset_collections@
58
59 @more_info@
60
61 </help>
62 </tool>