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1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0">
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2 <description>revert the original base qualities and add the mate cigar tag</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13
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14 java -jar \$JAVA_JAR_PATH/picard.jar
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15 RevertOriginalBaseQualitiesAndAddMateCigar
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16
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17 INPUT="${inputFile}"
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18 OUTPUT="${outFile}"
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19
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20 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
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21 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
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22
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23 SORT_ORDER=coordinate
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24 VALIDATION_STRINGENCY="${validation_stringency}"
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25 QUIET=true
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26 VERBOSITY=ERROR
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27
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28 </command>
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29 <inputs>
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30 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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31 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
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32 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
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33
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34 <expand macro="VS" />
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35
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36 </inputs>
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37
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38 <outputs>
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39 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
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45 <param name="restore_original_qualities" value="True"/>
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46 <param name="max_records_to_examine" value="10000"/>
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47 <param name="validation_stringency" value="LENIENT"/>
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48 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/>
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49 </test>
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50 </tests>
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51
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52 <stdio>
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53 <exit_code range="1:" level="fatal"/>
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54 </stdio>
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55
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56 <help>
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57
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58 **Purpose**
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59
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60 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.
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61
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62 @dataset_collections@
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63
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64 @description@
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65
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66 RESTORE_ORIGINAL_QUALITIES=Boolean
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67 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available.
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68 Default value: true. Possible values: {true, false}
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69
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70 MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not
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71 output, given that there are a no original base qualities (if we are to restore) and mate
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72 cigars exist. Set to 0 to never skip the file. Default value: 10000.
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73
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74 @more_info@
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75
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76 </help>
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77 </tool>
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78
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79
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