/
picard_FixMateInformation.xml
85 lines (60 loc) · 2.82 KB
/
picard_FixMateInformation.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
<tool name="FixMateInformation" id="picard_FixMateInformation" version="1.126.0">
<description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
<requirements>
<requirement type="package" version="1.126.0">picard</requirement>
</requirements>
<macros>
<import>picard_macros.xml</import>
</macros>
<command>
@java_options@
java -jar \$JAVA_JAR_PATH/picard.jar
FixMateInformation
INPUT="${inputFile}"
OUTPUT="${outFile}"
ASSUME_SORTED=${assume_sorted}
ADD_MATE_CIGAR=${add_mate_cigar}
SORT_ORDER=coordinate
VALIDATION_STRINGENCY="${validation_stringency}"
QUIET=true
VERBOSITY=ERROR
</command>
<inputs>
<param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
<param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
<param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
<expand macro="VS" />
</inputs>
<outputs>
<data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
</outputs>
<tests>
<test>
<param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
<param name="add_mate_cigar" value="True"/>
<param name="assume_sorted" value="False"/>
<param name="validation_stringency" value="LENIENT"/>
<output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
</test>
</tests>
<stdio>
<exit_code range="1:" level="fatal"/>
</stdio>
<help>
**Purpose**
Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.
------
.. class:: warningmark
**Warning on using ASSUME_SORTED option**
Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb
is to assume that the BAM you are working with is coordinate sorted.
@dataset_collections@
@description@
ASSUME_SORTED=Boolean
AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
otherwise. Default value: false.
ADD_MATE_CIGAR=Boolean
MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
@more_info@
</help>
</tool>