annotate picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 5:3d4f1fa26f0e draft

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