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comparison picard_CleanSam.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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-1:000000000000 0:5166ed57b1c4
1 <tool id="picard_CleanSam" name="CleanSam" version="1.135">
2 <description>perform SAM/BAM grooming</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9 java -jar \$JAVA_JAR_PATH/picard.jar
10 CleanSam
11 INPUT="${inputFile}"
12 OUTPUT="${outFile}"
13 QUIET=true
14 VERBOSITY=ERROR
15 VALIDATION_STRINGENCY=${validation_stringency}
16 </command>
17
18 <inputs>
19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
20
21 <expand macro="VS" />
22
23 </inputs>
24
25 <outputs>
26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
27 </data>
28 </outputs>
29
30 <stdio>
31 <exit_code range="1:" level="fatal"/>
32 </stdio>
33
34 <tests>
35 <test>
36 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
37 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
38 </test>
39 </tests>
40
41 <help>
42
43 .. class:: infomark
44
45 **Purpose**
46
47 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
48
49 1. to soft-clip an alignment that hangs off the end of its reference sequence.
50 2. to set MAPQ to 0 if a read is unmapped.
51
52 @dataset_collections@
53
54 @more_info@
55
56 </help>
57 </tool>