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