Mercurial > repos > devteam > picard
comparison picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 5:3d4f1fa26f0e draft
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author | devteam |
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date | Tue, 16 Dec 2014 19:03:21 -0500 |
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children | 3a3234d7a2e8 |
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4:ab1f60c26526 | 5:3d4f1fa26f0e |
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1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0"> | |
2 <description>revert the original base qualities and add the mate cigar tag</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.126.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 <command> | |
12 @java_options@ | |
13 | |
14 java -jar \$JAVA_JAR_PATH/picard.jar | |
15 RevertOriginalBaseQualitiesAndAddMateCigar | |
16 | |
17 INPUT="${inputFile}" | |
18 OUTPUT="${outFile}" | |
19 | |
20 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" | |
21 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" | |
22 | |
23 SORT_ORDER=coordinate | |
24 VALIDATION_STRINGENCY="${validation_stringency}" | |
25 QUIET=true | |
26 VERBOSITY=ERROR | |
27 | |
28 </command> | |
29 <inputs> | |
30 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
31 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> | |
32 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> | |
33 | |
34 <expand macro="VS" /> | |
35 | |
36 </inputs> | |
37 | |
38 <outputs> | |
39 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> | |
40 </outputs> | |
41 | |
42 <tests> | |
43 <test> | |
44 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> | |
45 <param name="restore_original_qualities" value="True"/> | |
46 <param name="max_records_to_examine" value="10000"/> | |
47 <param name="validation_stringency" value="LENIENT"/> | |
48 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> | |
49 </test> | |
50 </tests> | |
51 | |
52 <stdio> | |
53 <exit_code range="1:" level="fatal"/> | |
54 </stdio> | |
55 | |
56 <help> | |
57 | |
58 **Purpose** | |
59 | |
60 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. | |
61 | |
62 @dataset_collections@ | |
63 | |
64 @description@ | |
65 | |
66 RESTORE_ORIGINAL_QUALITIES=Boolean | |
67 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. | |
68 Default value: true. Possible values: {true, false} | |
69 | |
70 MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not | |
71 output, given that there are a no original base qualities (if we are to restore) and mate | |
72 cigars exist. Set to 0 to never skip the file. Default value: 10000. | |
73 | |
74 @more_info@ | |
75 | |
76 </help> | |
77 </tool> | |
78 | |
79 |