Mercurial > repos > devteam > picard
annotate picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 11:efc56ee1ade4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:23:17 -0500 |
| parents | 3a3234d7a2e8 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>revert the original base qualities and add the mate cigar tag</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
6 <expand macro="requirements" /> |
| 5 | 7 <command> |
| 8 @java_options@ | |
| 9 | |
| 10 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 11 RevertOriginalBaseQualitiesAndAddMateCigar | |
| 12 | |
| 13 INPUT="${inputFile}" | |
| 14 OUTPUT="${outFile}" | |
| 15 | |
| 16 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" | |
| 17 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" | |
| 18 | |
| 19 SORT_ORDER=coordinate | |
| 20 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 21 QUIET=true | |
| 22 VERBOSITY=ERROR | |
| 23 | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
| 27 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> | |
| 28 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> | |
| 29 | |
| 30 <expand macro="VS" /> | |
| 31 | |
| 32 </inputs> | |
| 33 | |
| 34 <outputs> | |
| 35 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> | |
| 36 </outputs> | |
| 37 | |
| 38 <tests> | |
| 39 <test> | |
| 40 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> | |
| 41 <param name="restore_original_qualities" value="True"/> | |
| 42 <param name="max_records_to_examine" value="10000"/> | |
| 43 <param name="validation_stringency" value="LENIENT"/> | |
| 44 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> | |
| 45 </test> | |
| 46 </tests> | |
| 47 | |
| 48 <stdio> | |
| 49 <exit_code range="1:" level="fatal"/> | |
| 50 </stdio> | |
| 51 | |
| 52 <help> | |
| 53 | |
| 54 **Purpose** | |
| 55 | |
| 56 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. | |
| 57 | |
| 58 @dataset_collections@ | |
| 59 | |
| 60 @description@ | |
| 61 | |
| 62 RESTORE_ORIGINAL_QUALITIES=Boolean | |
| 63 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. | |
| 64 Default value: true. Possible values: {true, false} | |
| 65 | |
| 66 MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not | |
| 67 output, given that there are a no original base qualities (if we are to restore) and mate | |
| 68 cigars exist. Set to 0 to never skip the file. Default value: 10000. | |
| 69 | |
| 70 @more_info@ | |
| 71 | |
| 72 </help> | |
| 73 </tool> | |
| 74 | |
| 75 |