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1 <tool id="bamSplitRef" name="Split BAM by Reference" version="2.4.0">
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2 <description>into dataset list collection</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 -reference
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11 -in localbam.bam
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12 -stub split_bam
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13 ## Preserve order from metadata in the output collection
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14 #import re
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15 #set $name = $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name))
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16 #if str($refs) != 'None':
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17 #set $ref_list = ' '.join(str($refs).split(","))
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18 #else
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19 #set $ref_list = ' '.join([$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')])
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20 #end if
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21 && mkdir -p outputs
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22 && (export I=0;
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23 for i in $ref_list;
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24 do I=\$((++I)); SN=`printf "split_bam.REF_%s.bam" "\$i"`;
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25 if [ -e \$SN ]; then FN=`printf "outputs/split_bam%05d%s.%s.bam" \$((I)) '$name' "\$i"`; mv \$SN \$FN; fi;
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26 done)
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
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31 <param name="refs" type="select" optional="True" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" >
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32 <help><![CDATA[Click and type in the box above to see options. You can select multiple entries.
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33 If "No options available" is displayed, you need to re-detect metadata on the input dataset.
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34 ]]></help>
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35 <options>
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36 <filter type="data_meta" ref="input_bam" key="reference_names" />
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37 </options>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <collection name="output_bams" type="list" label="${input_bam.name} Split List">
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42 <discover_datasets pattern="split_bam\d*(?P<designation>.+)\.bam" ext="bam" directory="outputs" visible="false"/>
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43 </collection>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input_bam" ftype="bam" value="bamtools-input2.bam"/>
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48 <output_collection name="output_bams" type="list">
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49 <element name="bamtools_input2.chr1" file="bamtools_input2.chr1" compare="sim_size" delta="500" />
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50 </output_collection>
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51 </test>
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52 </tests>
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53 <help>
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54 **What is does**
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55
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56 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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57
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58 -----
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59
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60 .. class:: warningmark
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61
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62 **DANGER: Multiple Outputs**
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63
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64 As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.
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65
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66 -----
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67
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68 **How it works**
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69
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70 Split alignments by reference name into a dataset list collection. The collection will be in the same order as the input BAM references.
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71
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72 In cases of unfinished genomes with very large number of reference sequences (scaffolds)
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73 it can generate thousands (if not millions) of output datasets.
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74
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75
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76 -----
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77
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78 .. class:: infomark
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79
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80 **More information**
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81
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82 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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83
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84 </help>
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85 <citations>
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86 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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87 </citations>
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88 </tool>
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