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comparison picard_CleanSam.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_CleanSam" name="CleanSam" version="1.126.0">
2
3 <description>perform SAM/BAM grooming</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 CleanSam
17 INPUT="${inputFile}"
18 OUTPUT="${outFile}"
19 QUIET=true
20 VERBOSITY=ERROR
21 VALIDATION_STRINGENCY=${validation_stringency}
22 </command>
23
24 <inputs>
25 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
26
27 <expand macro="VS" />
28
29 </inputs>
30
31 <outputs>
32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
33 </data>
34 </outputs>
35
36 <stdio>
37 <exit_code range="1:" level="fatal"/>
38 </stdio>
39
40 <tests>
41 <test>
42 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
43 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
44 </test>
45 </tests>
46
47 <help>
48
49 .. class:: infomark
50
51 **Purpose**
52
53 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
54
55 1. to soft-clip an alignment that hangs off the end of its reference sequence.
56 2. to set MAPQ to 0 if a read is unmapped.
57
58 @dataset_collections@
59
60 @more_info@
61
62 </help>
63 </tool>