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comparison picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
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