Mercurial > repos > devteam > picard

annotate picard_ReplaceSamHeader.xml @ 19:5053a18d9bc8 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 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents 465cbb0cf2eb
children 2a17c789e0a5
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: 14
diff changeset
1 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
2 <description>replace header in a SAM/BAM dataset</description>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
4 <import>picard_macros.xml</import>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
5 <token name="@WRAPPER_VERSION@">0</token>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
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: 2
diff changeset
9 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
10 @symlink_element_identifier@
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
11
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
12 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
13 #set $fasta_file="local_fasta.fa"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
14 ln -s "${inputFile}" "${fasta_file}" &&
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
16 picard
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
17 ReplaceSamHeader
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
18
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
19 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
20 HEADER="${header}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
21 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
22
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
23 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
24 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
26 ]]></command>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
27 <inputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
28 <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"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
29 <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"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
30 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
31
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
32 <outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
34 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
35
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
36 <tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
37 <test>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
38 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
39 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
40 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
41 </test>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
42 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
43
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
44
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
45 <help>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
46
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
47 **Purpose**
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
48
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
49 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.
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
50 @dataset_collections@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
51
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
52 @description@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
53
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
54 HEADER=File SAM file from which SAMFileHeader will be read. Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
55
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
56 @more_info@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
57
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
58 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
59 <expand macro="citations" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
60 </tool>