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1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="0.2.4">
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2 <requirements>
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3 <requirement type="binary">sambamba</requirement>
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4 </requirements>
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5 <description>
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6 on flags, fields, and tags
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7 </description>
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8 <command>
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9 #if $query != None:
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10 #set $query = $query.replace('__sq__', '\'')
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11 #set $query = $query.replace('__ob__', '[')
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12 #set $query = $query.replace('__cb__', ']')
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13 #set $query = $query.replace('__dq__', '"')
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14 #set $query = $query.replace('__oc__', '{')
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15 #set $query = $query.replace('__cc__', '}')
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16 #set $query = $query.replace('__gt__', chr(62))
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17 #set $query = $query.replace('__lt__', chr(60))
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18 #end if
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19 #if isinstance($input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__):
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20 #set $input1 = 'input.bam'
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21 ln -s $input $input1 &&
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22 ln -s $input.metadata.bam_index input.bai &&
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23 sambamba view -h --filter="$query" -f $outputformat.format -o $outfile $input1 $region
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24 #else
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25 sambamba view -S -h --filter="$query" -f $outputformat.format -o $outfile $input
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26 #end if
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27 </command>
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28 <inputs>
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29 <param name="input" type="data" format="bam,sam" label="BAM or SAM file to filter"/>
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30 <param name="query" type="text" size="80">
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31 <label>Filter expression</label>
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32 <help>
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33 The syntax is described at sambamba wiki: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
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34 </help>
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35 </param>
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36
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37 <conditional name="outputformat">
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38 <param name="format" type="select">
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39 <label>Output format</label>
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40 <option value="sam">SAM</option>
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41 <option value="bam">BAM</option>
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42 </param>
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43 <when value="sam">
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44 <!-- TODO
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45 <param name="header" type="select">
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46 <label>Include SAM header in output</label>
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47 <option value="yes">Yes</option>
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48 <option value="no">No</option>
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49 </param>-->
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50 </when>
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51 <when value="bam"/>
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52 </conditional>
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53 <param name="region" type="text" size="40" label="Region in format chr:beg-end, works for BAM input only">
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54 <help>
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55 The syntax is the same as in samtools, start and end coordinates are 1-based.
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56 </help>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data name="outfile" format="bam">
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61 <change_format>
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62 <when input="outputformat.format" value="sam" format="sam"/>
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63 </change_format>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="input" value="ex1_header.sam" ftype="sam" />
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69 <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
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70 <param name="format" value="bam" />
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71 <param name="region" value="" />
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72 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" />
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73 </test>
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74 <test>
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75 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
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76 <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />
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77 <param name="format" value="sam" />
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78 <!--<param name="header" value="yes" />-->
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79 <param name="region" value="AL096846:1000-5000" />
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80 <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" />
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81 </test>
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82 </tests>
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83 <help>
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84 **What it does**
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85
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86 This tool uses sambamba view to filter BAM/SAM on flags, fields, tags, and region.
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87 In order to install sambamba, visit its website_ and either download
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88 a Debian package for your architecture, or build the tool from source.
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89
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90 Input is SAM or BAM file, output is chosen by user.
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91
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92 **Note**
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93
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94 Filtering by region works only for coordinate-sorted BAM files. For SAM files this parameter is ignored.
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95
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96 -----
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97
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98 .. _website: http://github.com/lomereiter/sambamba
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99
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100
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101 </help>
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102 </tool>
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