annotate picard_FixMateInformation.xml @ 11:efc56ee1ade4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:23:17 -0500
parents 3a3234d7a2e8
children 05087b27692a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0">
5
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 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
6 <expand macro="requirements" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 <command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 FixMateInformation
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 ASSUME_SORTED=${assume_sorted}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 ADD_MATE_CIGAR=${add_mate_cigar}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <param name="add_mate_cigar" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="assume_sorted" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 .. class:: warningmark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 **Warning on using ASSUME_SORTED option**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 is to assume that the BAM you are working with is coordinate sorted.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 ASSUME_SORTED=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 otherwise. Default value: false.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 ADD_MATE_CIGAR=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81