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comparison picard_FixMateInformation.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="FixMateInformation" id="picard_FixMateInformation" version="1.126.0">
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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 FixMateInformation
16 INPUT="${inputFile}"
17 OUTPUT="${outFile}"
18 ASSUME_SORTED=${assume_sorted}
19 ADD_MATE_CIGAR=${add_mate_cigar}
20
21 SORT_ORDER=coordinate
22 VALIDATION_STRINGENCY="${validation_stringency}"
23 QUIET=true
24 VERBOSITY=ERROR
25
26 </command>
27 <inputs>
28 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
29 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
30 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
31
32 <expand macro="VS" />
33
34 </inputs>
35
36 <outputs>
37 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
43 <param name="add_mate_cigar" value="True"/>
44 <param name="assume_sorted" value="False"/>
45 <param name="validation_stringency" value="LENIENT"/>
46 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
47 </test>
48 </tests>
49
50 <stdio>
51 <exit_code range="1:" level="fatal"/>
52 </stdio>
53
54 <help>
55
56 **Purpose**
57
58 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.
59
60 ------
61
62 .. class:: warningmark
63
64 **Warning on using ASSUME_SORTED option**
65
66 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
67 is to assume that the BAM you are working with is coordinate sorted.
68
69 @dataset_collections@
70
71 @description@
72
73 ASSUME_SORTED=Boolean
74 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
75 otherwise. Default value: false.
76
77 ADD_MATE_CIGAR=Boolean
78 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
79
80 @more_info@
81
82 </help>
83 </tool>
84
85