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1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="1.135">
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2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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
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10 java -jar \$JAVA_JAR_PATH/picard.jar
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11 FixMateInformation
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12 INPUT="${inputFile}"
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13 OUTPUT="${outFile}"
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14 ASSUME_SORTED=${assume_sorted}
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15 ADD_MATE_CIGAR=${add_mate_cigar}
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16
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17 SORT_ORDER=coordinate
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18 VALIDATION_STRINGENCY="${validation_stringency}"
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19 QUIET=true
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20 VERBOSITY=ERROR
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21
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22 </command>
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23 <inputs>
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24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
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26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
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27
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28 <expand macro="VS" />
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29
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30 </inputs>
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31
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32 <outputs>
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33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
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39 <param name="add_mate_cigar" value="True"/>
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40 <param name="assume_sorted" value="False"/>
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41 <param name="validation_stringency" value="LENIENT"/>
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42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
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43 </test>
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44 </tests>
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45
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46 <stdio>
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47 <exit_code range="1:" level="fatal"/>
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48 </stdio>
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49
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50 <help>
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51
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52 **Purpose**
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53
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54 Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.
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55
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56 ------
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57
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58 .. class:: warningmark
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59
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60 **Warning on using ASSUME_SORTED option**
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61
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62 Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb
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63 is to assume that the BAM you are working with is coordinate sorted.
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64
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65 @dataset_collections@
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66
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67 @description@
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68
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69 ASSUME_SORTED=Boolean
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70 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
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71 otherwise. Default value: false.
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72
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73 ADD_MATE_CIGAR=Boolean
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74 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
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75
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76 @more_info@
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77
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78 </help>
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79 </tool>
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80
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81
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