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annotate sambamba.xml @ 1:6195f15d4541 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
author artbio
date Mon, 25 May 2020 17:10:17 -0400
parents
children 7ad3484aa5db
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6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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1 <tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.6">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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2 <description>
6195f15d4541 "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
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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4 </description>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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5 <requirements>
6195f15d4541 "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>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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7 </requirements>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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8 <stdio>
6195f15d4541 "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" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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10 </stdio>
6195f15d4541 "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> -->
6195f15d4541 "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[
6195f15d4541 "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 &&
6195f15d4541 "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 &&
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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15 #if $sambamba_options.selector == 'filter'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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16 sambamba view -h -t \${GALAXY_SLOTS:-4}
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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17 #if $sambamba_options.query != '':
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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18 --filter='$sambamba_options.query'
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19 #end if
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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20 -f '$format' -o $outfile input.bam $sambamba_options.region
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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21 #else
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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22 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$format'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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23 --subsampling-seed='$sambamba_options.seed'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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24 -s '$sambamba_options.fraction' -o '$outfile' input.bam
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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25 #end if
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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26 ]]></command>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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27 <inputs>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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28 <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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29 <param name="format" type="select" label="format of the tool output">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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30 <option value="bam">BAM</option>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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31 <option value="sam">SAM</option>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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32 </param>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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33 <conditional name="sambamba_options">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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34 <param name="selector" type="select" label="Filter or Down-sample alignments">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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35 <option value="sample">Down-sample bam or sam alignments</option>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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36 <option value="filter" selected="true">Filter bam or sam alignements</option>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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37 </param>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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38 <when value="filter">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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39 <param name="query" type="text" size="80">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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40 <sanitizer invalid_char="X">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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41 <valid initial="string.ascii_letters,string.digits, string.punctuation">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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42 <add value=" " />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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43 </valid>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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44 </sanitizer>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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45 <label>Filter expression</label>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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46 <help>See below for query syntax.</help>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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47 </param>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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48 <param name="region" type="text" size="40" label="Region in format chr:beg-end">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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49 <help>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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50 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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51 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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52 (region between 1,000,000 and 2,000,000bp including the end points).
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53 The coordinates are 1-based.
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54 </help>
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55 </param>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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56 </when>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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57 <when value="sample">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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58 <param name="seed" type="integer" value="123" size="10">
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59 <label>Seed value for randomisation</label>
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60 <help>
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61 Be careful at selecting different seed values if you
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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62 re-subsample a subsample output of this tool
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63 </help>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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64 </param>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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65 <param name="fraction" type="float" value="0.1" max="1" size="10" label="fraction to retrieve after subsampling">
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66 <help>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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67 Use a real number between 0 and 1 to indicate the relative size of
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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68 the fraction you wish to retrieve
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69 </help>
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70 </param>
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71 </when>
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72 </conditional>
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73 </inputs>
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74 <outputs>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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75 <data name="outfile" format="bam">
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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76 <change_format>
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77 <when input="format" value="sam" format="sam" />
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78 </change_format>
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79 </data>
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80 </outputs>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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81 <tests>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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82 <test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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83 <param name="input" value="ex1_header.sam" ftype="sam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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84 <param name="selector" value="filter" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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85 <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
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86 <param name="format" value="bam" />
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87 <param name="region" value="" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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88 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
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89 </test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
90 <test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
91 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
92 <param name="selector" value="filter" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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93 <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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94 <param name="format" value="sam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
parents:
diff changeset
95 <param name="region" value="AL096846:1000-5000" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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96 <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" lines_diff="2"/>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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97 </test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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98 <test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
99 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
100 <param name="selector" value="filter" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
101 <param name="query" value='' />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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102 <param name="format" value="sam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
103 <param name="region" value="AL096846:1000-5000" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
104 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
105 </test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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106 <test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
107 <param name="input" value="ex1_header.sam" ftype="sam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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108 <param name="selector" value="sample" />
6195f15d4541 "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="seed" value="123" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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110 <param name="fraction" value="0.1" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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111 <param name="format" value="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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112 <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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113 </test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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114 <test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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115 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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116 <param name="selector" value="sample" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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117 <param name="seed" value="123" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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118 <param name="fraction" value="0.1" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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119 <param name="format" value="sam" />
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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120 <output name="outfile" file="c1215_fixmate_sampled.sam" ftype="sam" lines_diff="2"/>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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121 </test>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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122 </tests>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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123 <help>
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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124 Sambamba Filter Overview
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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125 ========================
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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126
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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127 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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128
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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129
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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130 Filter Syntax
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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131 =============
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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132
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artbio
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133 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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134
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artbio
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135 *Basic condition* is a one for a single record field, tag, or flag.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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136
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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137 You can use ``==,`` ``!=,`` ``&gt;``, ``&lt;``, ``&gt;=``, ``&lt;=`` comparison operators for both integers and strings.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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138
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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139 Strings are delimited by single quotes, if you need a single quote inside a string, escape it with ``\\``.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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140
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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141 Examples of filter expressions
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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142 ------------------------------
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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143
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
144 ::
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
145
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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146 mapping_quality >= 30 and ([RG] =~ /^abcd/ or [NM] == 7)
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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147 read_name == 'abc\'def'
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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148
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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149 Basic conditions for flags
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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150 --------------------------
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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151
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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152 The following flag names are recognized:
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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153 * paired
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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154 * proper_pair
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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155 * unmapped
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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156 * mate_is_unmapped
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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157 * reverse_strand
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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158 * mate_is_reverse_strand
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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159 * first_of_pair
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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160 * second_of_pair
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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161 * secondary_alignment
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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162 * failed_quality_control
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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163 * duplicate
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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164
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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165 Example
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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166 ~~~~~~~
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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167
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
168 ::
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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169
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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diff changeset
170 not (unmapped or mate_is_unmapped) and first_of_pair
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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171
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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172 Basic conditions for fields
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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173 ---------------------------
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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174
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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175 Conditions for integer and string fields are supported.
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
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176
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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177 List of integer fields:
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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178 * ref_id
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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179 * position
6195f15d4541 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 516e8d55d6d45e6f2266805b78eb25a711621321"
artbio
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180 * mapping_quality
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181 * sequence_length
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182 * mate_ref_id
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183 * mate_position
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184 * template_length
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185
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186
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187 List of string fields:
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188 * read_name
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189 * sequence
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190 * cigar
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191
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192
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193 Example
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194 ~~~~~~~
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195
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196 ::
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197
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198 ref_id == 3 and mapping_quality >= 50 and sequence_length >= 80
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199
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200 Basic conditions for tags
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201 -------------------------
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202
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203 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.
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204
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205 In order to do filtering based on the presence of a particular tag, you can use special ``null`` value.
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206
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207 Example
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208 ~~~~~~~
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209
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210 ::
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211
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212 [RG] != null and [AM] == 37
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213
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214 Down-sampling
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215 =============
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216
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217 The tool is using the following sambamba command line for sampling:
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218
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219 ::
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220
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221 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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222 --subsampling-seed=&lt;an integer&gt;
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223 -s &lt;a real number between 0 and 1&gt; -o &lt;bam or sam output&gt; input_file
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224
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225 Warnings
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226 --------
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227
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228 The tool does not down-sample at a user given **number of lines**, because sambamba does not
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229 expose this functionality. For tool performances, we decided not to add it in this wrapper.
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230
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231 If you down-sample a dataset that has been *already down-sampled* with this tool, it is
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232 important that you choose **another seed** for randomisation. Otherwise, the new subsampling
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233 was reported not to conform the indicated fraction.
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234
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235
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236 .. _sambamba: http://github.com/lomereiter/sambamba
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237
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238 </help>
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239 <citations>
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240 <citation type="doi">10.1093/bioinformatics/btv098</citation>
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241 </citations>
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242 </tool>