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1 <tool id="sam_merge2" name="Merge BAM Files" version="1.1.2">
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2 <description>merges BAM files together</description>
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3 <requirements>
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4 <requirement type="package" version="1.56.0">picard</requirement>
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5 </requirements>
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6 <command>
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7 java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
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8 #for $i in $inputs
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9 I=${i.input}
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10 #end for
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11 2> $outlog
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12 || echo "Error running Picard MergeSamFiles" >&2
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13 </command>
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14 <inputs>
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15 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
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16 help="This name will appear in your history so use it to remember what the new file in your history contains" />
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17 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
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18 truevalue="true" falsevalue="false" checked="yes"
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19 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
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20 <param name="input1" label="First file" type="data" format="bam,sam" />
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21 <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
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22 <repeat name="inputs" title="Input Files">
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23 <param name="input" label="Add file" type="data" format="bam,sam" />
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24 </repeat>
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25 </inputs>
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26 <outputs>
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27 <data format="bam" name="output1" label="${title}.bam" />
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28 <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
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29 </outputs>
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30 <tests>
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31 <!-- TODO: add ability to test framework to test without at least
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32 one repeat element value
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33 -->
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34 <test>
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35 <param name="title" value="test1" />
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36 <param name="mergeSD" value="true" />
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37 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
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38 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
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39 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
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40 <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
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41 </test>
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42 <test>
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43 <param name="title" value="test2" />
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44 <param name="mergeSD" value="true" />
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45 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
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46 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
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47 <param name="input" value="sam_merge_in3.bam" ftype="bam" />
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48 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
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49 <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
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50 </test>
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51 </tests>
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52 <help>
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53
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54 **What it does**
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55
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56 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
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57 metadata such as read groups
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58
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59 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
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60
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61 </help>
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62 </tool>
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