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annotate picard_AddCommentsToBam.xml @ 7:08f69add4d06 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 15:11:36 -0500
parents 2589e6207cb4
children e417b1d6288d
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0">
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2 <description>add comments to 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 detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 picard
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10 AddCommentsToBam
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11 INPUT="${inputFile}"
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12 OUTPUT="${outFile}"
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13 #for $element in $comments:
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14 COMMENT="${element.comment}"
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15 #end for
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16 QUIET=true
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17 VERBOSITY=ERROR
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18 VALIDATION_STRINGENCY=${validation_stringency}
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19 ]]></command>
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21 <inputs>
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22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
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24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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25 </repeat>
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27 <expand macro="VS" />
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29 </inputs>
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31 <outputs>
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32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
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33 </outputs>
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36 <tests>
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37 <test>
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38 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
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39 <param name="comment" value="test1" />
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40 <param name="validation_stringency" value="LENIENT" />
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41 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
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42 </test>
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43 </tests>
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44 <help>
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46 .. class:: infomark
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48 **Purpose**
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50 Adds one or more comments (@CO) to the header of a specified BAM dataset.
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52 @dataset_collections@
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54 @description@
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56 COMMENT=String
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57 C=String Comments to add to the BAM file This option may be specified 0 or more times.
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59 @more_info@
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60 </help>
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61 </tool>
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