Mercurial > repos > avowinkel > picard

comparison picard_FixMateInformation.xml @ 0:5166ed57b1c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5166ed57b1c4
1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="1.135">
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9
10 java -jar \$JAVA_JAR_PATH/picard.jar
11 FixMateInformation
12 INPUT="${inputFile}"
13 OUTPUT="${outFile}"
14 ASSUME_SORTED=${assume_sorted}
15 ADD_MATE_CIGAR=${add_mate_cigar}
16
17 SORT_ORDER=coordinate
18 VALIDATION_STRINGENCY="${validation_stringency}"
19 QUIET=true
20 VERBOSITY=ERROR
21
22 </command>
23 <inputs>
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
27
28 <expand macro="VS" />
29
30 </inputs>
31
32 <outputs>
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
34 </outputs>
35
36 <tests>
37 <test>
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
39 <param name="add_mate_cigar" value="True"/>
40 <param name="assume_sorted" value="False"/>
41 <param name="validation_stringency" value="LENIENT"/>
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
43 </test>
44 </tests>
45
46 <stdio>
47 <exit_code range="1:" level="fatal"/>
48 </stdio>
49
50 <help>
51
52 **Purpose**
53
54 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.
55
56 ------
57
58 .. class:: warningmark
59
60 **Warning on using ASSUME_SORTED option**
61
62 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
63 is to assume that the BAM you are working with is coordinate sorted.
64
65 @dataset_collections@
66
67 @description@
68
69 ASSUME_SORTED=Boolean
70 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
71 otherwise. Default value: false.
72
73 ADD_MATE_CIGAR=Boolean
74 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
75
76 @more_info@
77
78 </help>
79 </tool>
80
81