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comparison picard_ReplaceSamHeader.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
comparison
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11:efc56ee1ade4 12:05087b27692a
2 <description>replace header in a SAM/BAM dataset</description> 2 <description>replace header in a SAM/BAM dataset</description>
3 <macros> 3 <macros>
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> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
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}" "${fasta_file}" &amp;&amp; 13 ln -s "${inputFile}" "${fasta_file}" &&
14 14
15 java -jar \$JAVA_JAR_PATH/picard.jar 15 picard
16 ReplaceSamHeader 16 ReplaceSamHeader
17 17
18 INPUT="${inputFile}" 18 INPUT="${inputFile}"
19 HEADER="${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
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 <stdio>
44 <exit_code range="1:" level="fatal"/>
45 </stdio>
46 43
47 <help> 44 <help>
48 45
49 **Purpose** 46 **Purpose**
50 47