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1 <tool id="bamSplitPaired" name="Split BAM by Paired/Single End" version="2.4.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.4.0">bamtools</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 ln -s '${input_bam}' 'localbam.bam' &&
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9 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
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10 bamtools split -paired
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11 -in localbam.bam
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12 -stub split_bam
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by single_end/paired_end"/>
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17 </inputs>
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18 <outputs>
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19 <data format="bam" name="single" label="${input_bam.name} mapped" from_work_dir="split_bam.SINGLE_END.bam" />
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20 <data format="bam" name="paired" label="${input_bam.name} unmapped" from_work_dir="split_bam.PAIRED_END.bam" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_bam" ftype="bam" value="bamtools-input-paired.bam"/>
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25 <output name="single" file="split_bam.SINGLE_END.bam" compare="sim_size" delta="200" />
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26 <output name="paired" file="split_bam.PAIRED_END.bam" compare="sim_size" delta="200" />
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27 </test>
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28 </tests>
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29 <help>
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30 **What is does**
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31
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32 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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33
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34 -----
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35
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36 .. class:: warningmark
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37
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38
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39 **How it works**
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40
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41
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42 Splits the input BAM file into 2 output files named (SINGLE_END) and (PAIRED_END) containing single_end and paired_end reads, respectively.
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43
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44 -----
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45
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46 .. class:: infomark
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47
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48 **More information**
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49
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50 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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51
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52 </help>
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53 <citations>
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54 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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55 </citations>
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56 </tool>
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