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annotate sambamba.xml @ 2:b13eb145dbd0 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
author artbio
date Thu, 30 Dec 2021 02:05:42 +0000
parents 3fc79704f0c0
children 29ec59ebff24
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2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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1 <tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0">
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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2 <description>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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3 on flags, fields, and tags using Sambamba
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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4 </description>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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5 <requirements>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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6 <requirement type="package" version="0.7.1">sambamba</requirement>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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7 </requirements>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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8 <stdio>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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9 <exit_code range="1:" level="fatal" description="Error occured" />
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10 </stdio>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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11 <!-- <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> -->
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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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 &&
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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14 ln -s $input.metadata.bam_index input.bai &&
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b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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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 $sambamba_options.query != '':
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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19 --filter='$sambamba_options.query'
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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20 #end if
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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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
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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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'
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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26 --subsampling-seed='$sambamba_options.seed'
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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27 -s '$sambamba_options.fraction'
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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28 -o '$outfile' input.bam
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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29
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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30 #else
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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31 sambamba slice -o '$outfile' input.bam $sambamba_options.region
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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32 #end if
1
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33 ]]></command>
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34 <inputs>
2
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35 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/>
1
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36 <conditional name="sambamba_options">
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37 <param name="selector" type="select" label="Filter, Down-sample or slice alignments">
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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38 <option value="sample">Down-sample bam or sam alignments</option>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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39 <option value="filter" selected="true">Filter bam or sam alignements</option>
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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40 <option value="slice">Slice bam or sam alignements by chromosome or chromosome region</option>
1
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41 </param>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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42 <when value="filter">
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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43 <param name="format" type="select" label="format of the tool output">
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44 <option value="bam">BAM</option>
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45 <option value="sam">SAM</option>
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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46 </param>
1
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47 <param name="query" type="text" size="80">
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48 <sanitizer invalid_char="X">
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49 <valid initial="string.ascii_letters,string.digits, string.punctuation">
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50 <add value=" " />
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51 </valid>
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52 </sanitizer>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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53 <label>Filter expression</label>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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54 <help>See below for query syntax.</help>
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55 </param>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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56 <param name="region" type="text" size="40" label="Region in format chr:beg-end">
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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57 <help>
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58 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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59 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
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60 (region between 1,000,000 and 2,000,000bp including the end points).
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61 The coordinates are 1-based.
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62 </help>
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63 </param>
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64 </when>
2
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65
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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66 <when value="slice">
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67 <param name="region" type="text" size="40" label="Region in format chr:beg-end">
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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68 <help>
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69 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
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70 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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71 (region between 1,000,000 and 2,000,000bp including the end points).
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72 The coordinates are 1-based. NOTE that sambamba slice only outputs
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73 BAM-format datasets.
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74 </help>
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75 </param>
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76 </when>
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77
1
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78 <when value="sample">
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
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79 <param name="format" type="select" label="format of the tool output">
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80 <option value="bam">BAM</option>
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81 <option value="sam">SAM</option>
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82 </param>
1
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83 <param name="seed" type="integer" value="123" size="10">
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84 <label>Seed value for randomisation</label>
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85 <help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
86 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"
artbio
parents:
diff changeset
87 re-subsample a subsample output of this tool
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
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88 </help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
89 </param>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
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90 <param name="fraction" type="float" value="0.1" max="1" size="10" label="fraction to retrieve after subsampling">
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
91 <help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
92 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
parents:
diff changeset
93 the fraction you wish to retrieve
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
94 </help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
95 </param>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
96 </when>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
97 </conditional>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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98 </inputs>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
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99 <outputs>
2
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artbio
parents: 1
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100 <data name="outfile" format="bam" label="Filter, slice or sample on ${on_string}">
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
101 <change_format>
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
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102 <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"
artbio
parents:
diff changeset
103 </change_format>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
104 </data>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
105 </outputs>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
106 <tests>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
107 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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108 <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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diff changeset
109 <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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diff changeset
110 <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"
artbio
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diff changeset
111 <param name="format" value="bam" />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
112 <param name="region" value="" />
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
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113 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" lines_diff="2"/>
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
114 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
115 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
116 <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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diff changeset
117 <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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diff changeset
118 <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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diff changeset
119 <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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diff changeset
120 <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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diff changeset
121 <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"
artbio
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diff changeset
122 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
123 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
124 <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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diff changeset
125 <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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diff changeset
126 <param name="query" value='' />
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
127 <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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128 <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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diff changeset
129 <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"
artbio
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130 </test>
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
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131 <test>
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
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132 <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"
artbio
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133 <param name="selector" value="slice" />
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
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134 <param name="query" value='' />
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
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135 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" />
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
diff changeset
136 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
diff changeset
137 </test>
1
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
138 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
139 <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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diff changeset
140 <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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diff changeset
141 <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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diff changeset
142 <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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143 <param name="format" value="bam" />
2
b13eb145dbd0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
artbio
parents: 1
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144 <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"
artbio
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145 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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146 <test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
147 <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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diff changeset
148 <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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diff changeset
149 <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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150 <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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diff changeset
151 <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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diff changeset
152 <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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diff changeset
153 </test>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
154 </tests>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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155 <help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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156 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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157 ========================
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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158
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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159 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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160
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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161
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artbio
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162 Filter Syntax
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163 =============
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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164
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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165 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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166
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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167 *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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168
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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169 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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170
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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171 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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172
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artbio
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173 Examples of filter expressions
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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174 ------------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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175
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artbio
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176 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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177
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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178 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"
artbio
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179 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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180
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artbio
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181 Basic conditions for flags
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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182 --------------------------
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"
artbio
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184 The following flag names are recognized:
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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185 * paired
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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186 * proper_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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187 * unmapped
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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188 * 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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189 * reverse_strand
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
190 * mate_is_reverse_strand
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
191 * first_of_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
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192 * second_of_pair
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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193 * secondary_alignment
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
194 * 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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195 * duplicate
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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196
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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197 Example
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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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
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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200 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
201
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
202 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"
artbio
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203
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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204 Basic conditions for fields
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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205 ---------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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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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diff changeset
207 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"
artbio
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208
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
209 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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210 * ref_id
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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211 * position
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
212 * mapping_quality
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
213 * sequence_length
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
214 * mate_ref_id
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
215 * mate_position
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
216 * template_length
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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217
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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218
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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219 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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220 * read_name
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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221 * sequence
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
222 * cigar
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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223
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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224
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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225 Example
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"
artbio
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227
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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228 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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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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diff changeset
230 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"
artbio
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231
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
232 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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233 -------------------------
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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234
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
235 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"
artbio
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236
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
237 In order to do filtering based on the presence of a particular tag, you can use special ``null`` value.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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238
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
239 Example
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
240 ~~~~~~~
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
241
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
242 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
243
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
244 [RG] != null and [AM] == 37
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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245
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
246 Down-sampling
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
247 =============
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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248
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
249 The tool is using the following sambamba command line for sampling:
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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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 ::
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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252
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
253 sambamba view -h -t &lt;number of Galaxy threads configured in job_conf.xml&gt; -f &lt;bam or sam&gt;
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
254 --subsampling-seed=&lt;an integer&gt;
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
255 -s &lt;a real number between 0 and 1&gt; -o &lt;bam or sam output&gt; input_file
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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256
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
257 Warnings
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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258 --------
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"
artbio
parents:
diff changeset
260 The tool does not down-sample at a user given **number of lines**, because sambamba does not
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
261 expose this functionality. For tool performances, we decided not to add it in this wrapper.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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262
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
263 If you down-sample a dataset that has been *already down-sampled* with this tool, it is
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
264 important that you choose **another seed** for randomisation. Otherwise, the new subsampling
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
265 was reported not to conform the indicated fraction.
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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266
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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268 .. _sambamba: http://github.com/lomereiter/sambamba
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269
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270 </help>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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271 <citations>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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272 <citation type="doi">10.1093/bioinformatics/btv098</citation>
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273 </citations>
3fc79704f0c0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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274 </tool>