Mercurial > repos > devteam > picard
annotate picard_FixMateInformation.xml @ 23:1cd1cf786389 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author | iuc |
---|---|
date | Thu, 16 May 2019 07:13:32 -0400 |
parents | 2a17c789e0a5 |
children | f9242e01365a |
rev | line source |
---|---|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
13
diff
changeset
|
1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
5 | 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> | |
20
2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents:
19
diff
changeset
|
5 <token name="@WRAPPER_VERSION@">1</token> |
5 | 6 </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
|
7 <expand macro="requirements" /> |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
5 | 9 @java_options@ |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
10 picard |
5 | 11 FixMateInformation |
12 INPUT="${inputFile}" | |
13 OUTPUT="${outFile}" | |
14 ASSUME_SORTED=${assume_sorted} | |
15 ADD_MATE_CIGAR=${add_mate_cigar} | |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
16 |
5 | 17 SORT_ORDER=coordinate |
18 VALIDATION_STRINGENCY="${validation_stringency}" | |
19 QUIET=true | |
20 VERBOSITY=ERROR | |
20
2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents:
19
diff
changeset
|
21 @TMPDIR_OPTION@ |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
22 |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
23 ]]></command> |
5 | 24 <inputs> |
25 <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"/> | |
26 <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"/> | |
27 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> | |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
28 |
5 | 29 <expand macro="VS" /> |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
30 |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
31 </inputs> |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
32 |
5 | 33 <outputs> |
34 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> | |
35 </outputs> | |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
36 |
5 | 37 <tests> |
38 <test> | |
39 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> | |
40 <param name="add_mate_cigar" value="True"/> | |
41 <param name="assume_sorted" value="False"/> | |
42 <param name="validation_stringency" value="LENIENT"/> | |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
43 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/> |
5 | 44 </test> |
45 </tests> | |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
46 |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
47 |
5 | 48 <help> |
49 | |
50 **Purpose** | |
51 | |
52 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. | |
53 | |
54 ------ | |
55 | |
56 .. class:: warningmark | |
57 | |
58 **Warning on using ASSUME_SORTED option** | |
59 | |
60 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 | |
61 is to assume that the BAM you are working with is coordinate sorted. | |
62 | |
63 @dataset_collections@ | |
64 | |
65 @description@ | |
66 | |
67 ASSUME_SORTED=Boolean | |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
68 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
69 otherwise. Default value: false. |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
70 |
5 | 71 ADD_MATE_CIGAR=Boolean |
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
72 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
73 |
5 | 74 @more_info@ |
75 | |
76 </help> | |
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
13
diff
changeset
|
77 <expand macro="citations" /> |
5 | 78 </tool> |