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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="1.135">
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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>
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8 @java_options@
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9 java -jar \$JAVA_JAR_PATH/picard.jar
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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=${validation_stringency}
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19 </command>
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20
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21 <inputs>
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22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
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24 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
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25 </repeat>
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26
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27 <expand macro="VS" />
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28
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29 </inputs>
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30
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31 <outputs>
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32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
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33 </outputs>
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34
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35 <stdio>
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36 <exit_code range="1:" level="fatal"/>
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37 </stdio>
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38
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39 <tests>
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40 <test>
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41 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
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42 <param name="comment" value="test1" />
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43 <param name="validation_stringency" value="LENIENT" />
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44 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
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45 </test>
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46 </tests>
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47 <help>
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48
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49 .. class:: infomark
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50
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51 **Purpose**
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52
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53 Adds one or more comments (@CO) to the header of a specified BAM dataset.
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54
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55 @dataset_collections@
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56
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57 @description@
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58
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59 COMMENT=String
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60 C=String Comments to add to the BAM file This option may be specified 0 or more times.
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61
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62 @more_info@
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63 </help>
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64 </tool>
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