Mercurial > repos > devteam > picard

annotate picard_ReplaceSamHeader.xml @ 23:4740a2548206 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:58:57 +0000
parents a5a13ea16d17
children e65f2d5fd3d8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
486d7500da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 9
diff changeset
1 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
23
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
2 <description>replace header in a SAM/BAM dataset</description>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
3 <xrefs>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
4 <xref type="bio.tools">picard_replacesamheader</xref>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
5 </xrefs>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
6 <macros>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
7 <import>picard_macros.xml</import>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
8 <token name="@WRAPPER_VERSION@">1</token>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
9 </macros>
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
10 <expand macro="requirements" />
4740a2548206 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 15
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
12 @java_options@
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
13 @symlink_element_identifier@
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
14
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
15 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
16 #set $fasta_file="local_fasta.fa"
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
17 ln -s "${inputFile}" "${fasta_file}" &&
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
18
7
08f69add4d06 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 3
diff changeset
19 picard
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
20 ReplaceSamHeader
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
21
9
41b8d087a2d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 8
diff changeset
22 INPUT='$escaped_element_identifier'
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
23 HEADER="${header}"
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
24 OUTPUT="${outFile}"
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
25
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
26 QUIET=true
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
27 VERBOSITY=ERROR
15
a5a13ea16d17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 14
diff changeset
28 @TMPDIR_OPTION@
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
29
7
08f69add4d06 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 3
diff changeset
30 ]]></command>
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
31 <inputs>
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
32 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
33 <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
34 </inputs>
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
35
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
36 <outputs>
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
37 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
38 </outputs>
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
39
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
40 <tests>
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
41 <test>
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
42 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
43 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
44 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
45 </test>
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
46 </tests>
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
47
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
48
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
49 <help>
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
50
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
51 **Purpose**
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
52
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
53 Replace the SAMFileHeader in a SAM/BAM dataset with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input datasets must be the same.
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
54 @dataset_collections@
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
55
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
56 @description@
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
57
8
e417b1d6288d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 7
diff changeset
58 HEADER=File SAM file from which SAMFileHeader will be read. Required.
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
59
3
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
60 @more_info@
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
61
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
62 </help>
14
486d7500da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 9
diff changeset
63 <expand macro="citations" />
0
ff4ec13e496e Uploaded tarball to repository
devteam
parents:
diff changeset
64 </tool>