annotate picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 24:b9fbec5ac6b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:52 -0400
parents 2a17c789e0a5
children f9242e01365a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>revert the original base qualities and add the mate cigar tag</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 RevertOriginalBaseQualitiesAndAddMateCigar
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
12
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13 INPUT='$inputFile'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
18
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 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
23 @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
24
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
25 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 <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
32
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
33 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
34
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
38
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <param name="restore_original_qualities" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <param name="max_records_to_examine" value="10000"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <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
45 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
48
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
49
5
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 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 RESTORE_ORIGINAL_QUALITIES=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
61 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
62 Default value: true. Possible values: {true, false}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
63
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
64 MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
65 output, given that there are a no original base qualities (if we are to restore) and mate
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 cigars exist. Set to 0 to never skip the file. Default value: 10000.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 13
diff changeset
71 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 </tool>