annotate picard_FixMateInformation.xml @ 7:379fdf4c41ac draft

Uploaded
author devteam
date Thu, 29 Jan 2015 16:11:15 -0500
parents 3d4f1fa26f0e
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="FixMateInformation" id="picard_FixMateInformation" version="1.126.0">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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 FixMateInformation
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 ASSUME_SORTED=${assume_sorted}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 ADD_MATE_CIGAR=${add_mate_cigar}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <param name="add_mate_cigar" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <param name="assume_sorted" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 .. class:: warningmark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 **Warning on using ASSUME_SORTED option**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 is to assume that the BAM you are working with is coordinate sorted.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 ASSUME_SORTED=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 otherwise. Default value: false.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 ADD_MATE_CIGAR=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85