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annotate picard_ReplaceSamHeader.xml @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
parents ff4ec13e496e
children 08f69add4d06
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1 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.0">
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2 <description>replace header in a SAM/BAM dataset</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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12 #set $fasta_file="local_fasta.fa"
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 ln -s "${inputFile}" "${fasta_file}" &amp;&amp;
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 java -jar \$JAVA_JAR_PATH/picard.jar
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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16 ReplaceSamHeader
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18 INPUT="${inputFile}"
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19 HEADER="${header}"
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20 OUTPUT="${outFile}"
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22 QUIET=true
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23 VERBOSITY=ERROR
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24
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25 </command>
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26 <inputs>
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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"/>
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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"/>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 </inputs>
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30
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31 <outputs>
3
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32 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
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38 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
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39 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
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40 </test>
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41 </tests>
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43 <stdio>
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44 <exit_code range="1:" level="fatal"/>
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45 </stdio>
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46
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47 <help>
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48
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49 **Purpose**
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50
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51 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.
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52 @dataset_collections@
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54 @description@
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56 HEADER=File SAM file from which SAMFileHeader will be read. Required.
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58 @more_info@
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59
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60 </help>
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61 </tool>
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