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1 <tool id="bamSplit" name="Split" version="0.0.1" force_history_refresh="True">
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2 <description>BAM datasets on variety of attributes</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
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5 </requirements>
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6 <command>
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7
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8 echo "BAM" > $report &&
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9
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10 #for $bam_count, $input_bam in enumerate( $input_bams ):
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11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
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12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
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13 #end for
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14
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15 bamtools
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16 split
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17
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18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
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19
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20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
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21
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22 #else
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23
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24 ${analysis_type.analysis_type_selector}
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25
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26 #end if
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27
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28 -stub split_bam
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29
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30 #for $bam_count, $input_bam in enumerate( $input_bams ):
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31 -in "localbam_${bam_count}.bam"
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32 #end for
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33
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34 </command>
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35
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36 <inputs>
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37 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
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38 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
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39 </repeat>
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40 <conditional name="analysis_type">
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41 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
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42 <option value="-mapped">Mapping status (-mapped)</option>
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43 <option value="-paired">Pairing status (-paired)</option>
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44 <option value="-reference">Reference name (-reference)</option>
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45 <option value="-tag">Specific tag (-tag)</option>
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46 </param>
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47 <when value="-tag">
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48 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/>
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49 </when>
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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54 <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
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55 <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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61 <param name="analysis_type_selector" value="-mapped"/>
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62 <output name="report">
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63 <assert_contents>
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64 <has_line line="BAM" />
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65 </assert_contents>
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66 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
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67 </output>
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68
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69 </test>
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70 </tests>
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71 <help>
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72 **What is does**
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73
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74 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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75
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76 -----
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77
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78 .. class:: warningmark
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79
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80 **DANGER: Multiple Outputs**
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81
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82 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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83
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84 -----
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85
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86 **How it works**
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87
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88 The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
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89
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90 Mapping status (-mapped) split mapped/unmapped and generate two output files
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91 named (MAPPED) and (UNMAPPED) containing mapped and unmapped
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92 reads, respectively.
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93
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94 Pairing status (-paired) split single-end/paired-end alignments and generate two output files
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95 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
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96 reads, respectively.
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97
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98 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with
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99 very large number of reference sequences (scaffolds) it can generate
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100 thousands (if not millions) of output datasets.
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101
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102 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this
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103 option from the menu will allow you to enter the tag name. As was the
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104 case with the reference splitting above, this option can produce very
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105 large number of outputs if a tag has a large number of unique values.
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106
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107 -----
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108
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109 .. class:: infomark
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110
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111 **More information**
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112
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113 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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114
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115 </help>
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116 <citations>
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117 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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118 </citations>
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119 </tool>
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