comparison picard_CleanSam.xml @ 30:5b53bf15be53 draft

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author devteam
date Thu, 13 Feb 2014 16:00:18 -0500
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29:71794c51e089 30:5b53bf15be53
1 <tool id="picard_cleansam" name="CleanSam" version="1.106.0">
2 <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CleanSam
3 Read SAM and perform various fix-ups. Currently, the only fix-ups are 1: to soft-clip an alignment that hangs off the end of its reference sequence; and 2: to set MAPQ to 0 if a read is unmapped.
4 -->
5 <description>Read SAM and perform various fix-ups.</description>
6
7 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
8
9 <command interpreter="bash">
10 cleansamwrapper.sh $input1 $output1
11 </command>
12
13 <inputs>
14 <param name="input1" type="data" format="sam" label="SAM File to clean" />
15 </inputs>
16
17 <outputs>
18 <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">
19 </data>
20 </outputs>
21
22 <tests>
23 <test>
24 <param name="input1" value="cleansamtestinput.sam" />
25 <output name="output1" file="cleansamtestoutput.sam" ftype="sam" />
26 </test>
27 </tests>
28
29 <help>
30
31 **What it does**
32
33 Read SAM and perform various fix-ups. Currently, the only fix-up it to soft-clip an alignment that hangs off the end of its reference sequence.
34
35 </help>
36 </tool>