Mercurial > repos > devteam > picard_122_up
comparison picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.122.0"> | |
2 <description>revert the original base qualities and add the mate cigar tag</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">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/RevertOriginalBaseQualitiesAndAddMateCigar.jar | |
15 | |
16 INPUT="${inputFile}" | |
17 OUTPUT="${outFile}" | |
18 | |
19 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" | |
20 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" | |
21 | |
22 SORT_ORDER=coordinate | |
23 VALIDATION_STRINGENCY="${validation_stringency}" | |
24 QUIET=true | |
25 VERBOSITY=ERROR | |
26 | |
27 </command> | |
28 <inputs> | |
29 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
30 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> | |
31 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> | |
32 | |
33 <expand macro="VS" /> | |
34 | |
35 </inputs> | |
36 | |
37 <outputs> | |
38 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> | |
39 </outputs> | |
40 | |
41 <tests> | |
42 <test> | |
43 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> | |
44 <param name="restore_original_qualities" value="True"/> | |
45 <param name="max_records_to_examine" value="10000"/> | |
46 <param name="validation_stringency" value="LENIENT"/> | |
47 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> | |
48 </test> | |
49 </tests> | |
50 | |
51 <stdio> | |
52 <exit_code range="1:" level="fatal"/> | |
53 </stdio> | |
54 | |
55 <help> | |
56 | |
57 **Purpose** | |
58 | |
59 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. | |
60 | |
61 @dataset_collections@ | |
62 | |
63 @description@ | |
64 | |
65 RESTORE_ORIGINAL_QUALITIES=Boolean | |
66 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. | |
67 Default value: true. Possible values: {true, false} | |
68 | |
69 MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not | |
70 output, given that there are a no original base qualities (if we are to restore) and mate | |
71 cigars exist. Set to 0 to never skip the file. Default value: 10000. | |
72 | |
73 @more_info@ | |
74 | |
75 </help> | |
76 </tool> | |
77 | |
78 |