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1 <tool id="sam_merge2" name="Merge BAM Files" version="1.2.0">
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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 <stdio>
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7 <exit_code range="1:" />
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8 <exit_code range=":-1" />
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9 <regex match="Error:" />
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10 <regex match="Exception:" />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 java -Xmx2G
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15 -jar \$JAVA_JAR_PATH/MergeSamFiles.jar
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16 MSD=$mergeSD
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17 VALIDATION_STRINGENCY=LENIENT
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18 O="$output1"
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19 TMP_DIR=$__new_file_path__
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20 #for $input in $inputs
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21 I="${input}"
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22 #end for
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="inputs" type="data" format="bam,sam" multiple="True" label="Files to merge" />
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27 <param name="mergeSD" type="boolean" label="Merge all component bam file headers into the merged bam file"
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28 truevalue="true" falsevalue="false" checked="yes"
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29 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
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30 </inputs>
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31 <outputs>
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32 <data format="bam" name="output1" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="mergeSD" value="true" />
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37 <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam" ftype="bam" />
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38 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
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39 </test>
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40 <test>
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41 <param name="mergeSD" value="true" />
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42 <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam,sam_merge_in3.bam" ftype="bam" />
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43 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48 **What it does**
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49
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50 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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51 metadata such as read groups.
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52
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53 .. _Picard: http://broadinstitute.github.io/picard/
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54 ]]>
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55 </help>
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56 </tool>
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