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1 <tool id="picard_cleansam" name="CleanSam" version="1.106.0">
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2 <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CleanSam
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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.
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4 -->
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5 <description>Read SAM and perform various fix-ups.</description>
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6
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7 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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8
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9 <command interpreter="bash">
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10 cleansamwrapper.sh $input1 $output1
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11 </command>
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12
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13 <inputs>
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14 <param name="input1" type="data" format="sam" label="SAM File to clean" />
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15 </inputs>
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16
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17 <outputs>
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18 <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">
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19 </data>
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20 </outputs>
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21
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22 <tests>
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23 <test>
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24 <param name="input1" value="cleansamtestinput.sam" />
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25 <output name="output1" file="cleansamtestoutput.sam" ftype="sam" />
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26 </test>
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27 </tests>
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28
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29 <help>
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30
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31 **What it does**
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32
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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.
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34
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35 </help>
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36 </tool> |
