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comparison picard_ReplaceSamHeader.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
comparison
equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9 @symlink_element_identifier@
10 10
11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa 11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
12 #set $fasta_file="local_fasta.fa" 12 #set $fasta_file="local_fasta.fa"
13 ln -s "${inputFile}" "${fasta_file}" && 13 ln -s "${inputFile}" "${fasta_file}" &&
14 14
15 picard 15 picard
16 ReplaceSamHeader 16 ReplaceSamHeader
17 17
18 INPUT="${inputFile}" 18 INPUT='$inputFile.element_identifier'
19 HEADER="${header}" 19 HEADER="${header}"
20 OUTPUT="${outFile}" 20 OUTPUT="${outFile}"
21 21
22 QUIET=true 22 QUIET=true
23 VERBOSITY=ERROR 23 VERBOSITY=ERROR
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/> 27 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
28 <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/> 28 <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
29 </inputs> 29 </inputs>
30 30
31 <outputs> 31 <outputs>
32 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/> 32 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
33 </outputs> 33 </outputs>
34 34
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/> 37 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
38 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/> 38 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
39 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/> 39 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
40 </test> 40 </test>
41 </tests> 41 </tests>
42 42
43 43
44 <help> 44 <help>
45 45
46 **Purpose** 46 **Purpose**
47 47
48 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. 48 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.
49 @dataset_collections@ 49 @dataset_collections@
50 50
51 @description@ 51 @description@
52 52
53 HEADER=File SAM file from which SAMFileHeader will be read. Required. 53 HEADER=File SAM file from which SAMFileHeader will be read. Required.
54 54
55 @more_info@ 55 @more_info@
56 56
57 </help> 57 </help>
58 </tool> 58 </tool>