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annotate sambamba.xml @ 3:29ec59ebff24 draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
author artbio
date Thu, 30 Dec 2021 17:44:02 +0000
parents b13eb145dbd0
children
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29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
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1 <tool id="sambamba_sample_or_filter" name="Sample, Slice or Filter BAM" version="0.7.1+galaxy1">
1
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2 <description>
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3 on flags, fields, and tags using Sambamba
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.7.1">sambamba</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error occured" />
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10 </stdio>
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11 <!-- <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> -->
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12 <command detect_errors="exit_code"><![CDATA[
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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13 ln -s $input input.bam &&
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14 ln -s $input.metadata.bam_index input.bai &&
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15
1
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16 #if $sambamba_options.selector == 'filter'
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17 sambamba view -h -t \${GALAXY_SLOTS:-4}
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18 #if $sambamba_options.query != '':
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19 --filter='$sambamba_options.query'
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20 #end if
2
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21 -f '$sambamba_options.format'
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22 -o $outfile input.bam $sambamba_options.region
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23
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24 #else if $sambamba_options.selector == 'sample'
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25 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format'
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26 --subsampling-seed='$sambamba_options.seed'
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27 -s '$sambamba_options.fraction'
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28 -o '$outfile' input.bam
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29 #end if
2
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30
3
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31 #if $sambamba_options.selector == 'slice'
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32 #if $sambamba_options.slice.slice_format == 'text'
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33 sambamba slice -o '$outfile' input.bam $sambamba_options.slice.region
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34 #else
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35 sambamba slice --regions $sambamba_options.slice.bed_file -o '$outfile' input.bam
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36 #end if
2
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37 #end if
1
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38 ]]></command>
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39 <inputs>
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40 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/>
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41 <conditional name="sambamba_options">
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42 <param name="selector" type="select" label="Filter, Down-sample or slice alignments">
1
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43 <option value="sample">Down-sample bam or sam alignments</option>
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44 <option value="filter" selected="true">Filter bam or sam alignements</option>
2
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45 <option value="slice">Slice bam or sam alignements by chromosome or chromosome region</option>
1
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46 </param>
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47 <when value="filter">
2
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48 <param name="format" type="select" label="format of the tool output">
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49 <option value="bam">BAM</option>
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50 <option value="sam">SAM</option>
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51 </param>
1
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52 <param name="query" type="text" size="80">
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53 <sanitizer invalid_char="X">
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54 <valid initial="string.ascii_letters,string.digits, string.punctuation">
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55 <add value=" " />
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56 </valid>
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57 </sanitizer>
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58 <label>Filter expression</label>
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59 <help>See below for query syntax.</help>
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60 </param>
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61 <param name="region" type="text" size="40" label="Region in format chr:beg-end">
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62 <help>
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63 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
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64 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
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65 (region between 1,000,000 and 2,000,000bp including the end points).
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66 The coordinates are 1-based.
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67 </help>
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68 </param>
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69 </when>
2
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70
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71 <when value="slice">
3
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72 <conditional name="slice">
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73 <param name="slice_format" type="select" label="specify in text field or a bed file">
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74 <option value="text">Specify in the region field</option>
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75 <option value="bed" selected="true">BED file</option>
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76 </param>
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77 <when value="bed">
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78 <param name="bed_file" type="data" format="bed" label="BED file"
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79 help="The coordinates are 0-based. NOTE that sambamba slice only outputs BAM-format datasets."/>
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80 </when>
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81 <when value="text">
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82 <param name="region" type="text" size="40" label="Region(s) in space-separated format chr:start-end">
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83 <help>
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84 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
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artbio
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85 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
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artbio
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86 (region between 1,000,000 and 2,000,000bp including the end points).
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artbio
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87 The coordinates are 1-based. NOTE that sambamba slice only outputs
29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
artbio
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88 BAM-format datasets.
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artbio
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89 </help>
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90 </param>
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artbio
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91 </when>
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artbio
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92 </conditional>
2
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artbio
parents: 1
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93 </when>
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artbio
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94
1
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95 <when value="sample">
2
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artbio
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96 <param name="format" type="select" label="format of the tool output">
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artbio
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97 <option value="bam">BAM</option>
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artbio
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98 <option value="sam">SAM</option>
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artbio
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99 </param>
1
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artbio
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100 <param name="seed" type="integer" value="123" size="10">
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artbio
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101 <label>Seed value for randomisation</label>
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artbio
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102 <help>
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103 Be careful at selecting different seed values if you
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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104 re-subsample a subsample output of this tool
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105 </help>
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106 </param>
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artbio
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107 <param name="fraction" type="float" value="0.1" max="1" size="10" label="fraction to retrieve after subsampling">
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artbio
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108 <help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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109 Use a real number between 0 and 1 to indicate the relative size of
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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110 the fraction you wish to retrieve
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111 </help>
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112 </param>
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
2
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artbio
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117 <data name="outfile" format="bam" label="Filter, slice or sample on ${on_string}">
1
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118 <change_format>
2
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119 <when input="sambamba_options['format']" value="sam" format="sam" />
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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120 </change_format>
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121 </data>
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122 </outputs>
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artbio
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123 <tests>
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artbio
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124 <test>
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artbio
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125 <param name="input" value="ex1_header.sam" ftype="sam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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126 <param name="selector" value="filter" />
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artbio
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127 <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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128 <param name="format" value="bam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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129 <param name="region" value="" />
2
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130 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" lines_diff="2"/>
1
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131 </test>
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132 <test>
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artbio
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133 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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134 <param name="selector" value="filter" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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135 <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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136 <param name="format" value="sam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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137 <param name="region" value="AL096846:1000-5000" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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138 <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" lines_diff="2"/>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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139 </test>
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140 <test>
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artbio
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141 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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142 <param name="selector" value="filter" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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143 <param name="query" value='' />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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144 <param name="format" value="sam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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145 <param name="region" value="AL096846:1000-5000" />
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artbio
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diff changeset
146 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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147 </test>
2
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148 <test>
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149 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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150 <param name="selector" value="slice" />
3
29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
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151 <param name="slice_format" value="text" />
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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152 <param name="query" value='' />
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153 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" />
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154 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
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155 </test>
3
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156 <test>
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157 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
artbio
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158 <param name="selector" value="slice" />
29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
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159 <param name="slice_format" value="bed" />
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160 <param name="query" value='' />
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161 <param name="bed_file" value="regions.bed" />
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162 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
29ec59ebff24 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
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163 </test>
1
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164 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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165 <param name="input" value="ex1_header.sam" ftype="sam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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166 <param name="selector" value="sample" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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167 <param name="seed" value="123" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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168 <param name="fraction" value="0.1" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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169 <param name="format" value="bam" />
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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170 <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" lines_diff="2"/>
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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171 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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172 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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173 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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174 <param name="selector" value="sample" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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175 <param name="seed" value="123" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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176 <param name="fraction" value="0.1" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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177 <param name="format" value="sam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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178 <output name="outfile" file="c1215_fixmate_sampled.sam" ftype="sam" lines_diff="2"/>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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179 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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180 </tests>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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181 <help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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182 Sambamba Filter Overview
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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183 ========================
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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184
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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185 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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186
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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187
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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188 Filter Syntax
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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189 =============
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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190
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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191 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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192
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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193 *Basic condition* is a one for a single record field, tag, or flag.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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194
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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195 You can use ``==,`` ``!=,`` ``&gt;``, ``&lt;``, ``&gt;=``, ``&lt;=`` comparison operators for both integers and strings.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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196
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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197 Strings are delimited by single quotes, if you need a single quote inside a string, escape it with ``\\``.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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198
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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199 Examples of filter expressions
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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200 ------------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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201
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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202 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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203
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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204 mapping_quality >= 30 and ([RG] =~ /^abcd/ or [NM] == 7)
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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205 read_name == 'abc\'def'
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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206
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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207 Basic conditions for flags
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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208 --------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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209
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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210 The following flag names are recognized:
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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211 * paired
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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212 * proper_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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213 * unmapped
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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214 * mate_is_unmapped
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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215 * reverse_strand
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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216 * mate_is_reverse_strand
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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217 * first_of_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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218 * second_of_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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219 * secondary_alignment
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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220 * failed_quality_control
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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221 * duplicate
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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222
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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223 Example
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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224 ~~~~~~~
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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225
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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226 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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227
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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228 not (unmapped or mate_is_unmapped) and first_of_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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229
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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230 Basic conditions for fields
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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231 ---------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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232
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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233 Conditions for integer and string fields are supported.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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234
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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235 List of integer fields:
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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236 * ref_id
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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237 * position
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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238 * mapping_quality
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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239 * sequence_length
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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240 * mate_ref_id
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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241 * mate_position
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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242 * template_length
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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243
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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244
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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245 List of string fields:
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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246 * read_name
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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247 * sequence
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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248 * cigar
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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249
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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250
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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251 Example
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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252 ~~~~~~~
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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253
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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254 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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255
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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256 ref_id == 3 and mapping_quality >= 50 and sequence_length >= 80
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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257
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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258 Basic conditions for tags
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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259 -------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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260
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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261 Tags are denoted by their names in square brackets, for instance, ``[RG]`` or ``[Q2].`` They support conditions for both integers and strings, i.e. the tag must also hold value of the corresponding type.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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262
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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263 In order to do filtering based on the presence of a particular tag, you can use special ``null`` value.
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264
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265 Example
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266 ~~~~~~~
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267
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268 ::
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269
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270 [RG] != null and [AM] == 37
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271
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272 Down-sampling
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273 =============
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274
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275 The tool is using the following sambamba command line for sampling:
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276
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277 ::
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278
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279 sambamba view -h -t &lt;number of Galaxy threads configured in job_conf.xml&gt; -f &lt;bam or sam&gt;
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280 --subsampling-seed=&lt;an integer&gt;
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281 -s &lt;a real number between 0 and 1&gt; -o &lt;bam or sam output&gt; input_file
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282
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283 Warnings
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284 --------
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285
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286 The tool does not down-sample at a user given **number of lines**, because sambamba does not
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287 expose this functionality. For tool performances, we decided not to add it in this wrapper.
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288
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289 If you down-sample a dataset that has been *already down-sampled* with this tool, it is
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290 important that you choose **another seed** for randomisation. Otherwise, the new subsampling
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291 was reported not to conform the indicated fraction.
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292
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293
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294 .. _sambamba: http://github.com/lomereiter/sambamba
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295
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296 </help>
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297 <citations>
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298 <citation type="doi">10.1093/bioinformatics/btv098</citation>
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299 </citations>
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300 </tool>