Mercurial > repos > artbio > artbio_bam_cleaning

annotate artbio_bam_cleaning.xml @ 8:b12e50bcddd2 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
author artbio
date Thu, 30 Dec 2021 19:53:07 +0000
parents 745f529127b8
children cb94e94e0f4e
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8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy1">
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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2 <description>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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3 on flags and PCR Duplicates and MD recalibration
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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4 </description>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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5 <macros>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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6 <import>macro.xml</import>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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7 </macros>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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8 <requirements>
7
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9 <requirement type="package" version="1.6=hb116620_7">samtools</requirement>
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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10 <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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11 <requirement type="package" version="1.3.5=py39hba5d119_3">freebayes</requirement>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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12 </requirements>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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13 <stdio>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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14 <exit_code range="1:" level="fatal" description="Error occured" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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15 </stdio>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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16 <command detect_errors="exit_code"><![CDATA[
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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17 @pipefail@
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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18 @set_fasta_index@
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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19 #set input_base = 'input'
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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20 ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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21 ln -s $input_bam input.bam &&
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22 sambamba view -h -t \${GALAXY_SLOTS:-2} --filter="mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)" -f "bam" ${input_base}".bam"
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23 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
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ebdaf5b3d6a7 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b846085c8b8e29bb067a3cdcb90355117aeebf42"
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24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
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b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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25 #if $specify_outputs == 'just_calMD':
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26 > $calmd
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b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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27 #else if $specify_outputs == 'calMDandMQ' or $specify_outputs == 'both':
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999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
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28 | tee $calmd
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
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29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
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30 #end if
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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31 ]]></command>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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32 <inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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33 <expand macro="reference_source_conditional" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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34 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
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b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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35 <param name="specify_outputs" type="select" label="specify cleaned output(s)"
7
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36 display="radio"
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37 help="The tool first generates MD-recalibrated alignements, then discards
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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38 aberrant Mapping Quality alignements generated by calMD recalibration.
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39 One, the other, or both types of outputs can be retained by the tool">
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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40 <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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41 <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded (for snv and small indel callers)</option>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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42 <option value="both">Both types of outputs are retained</option>
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43 </param>
0
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44 </inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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45 <outputs>
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46 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">
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47 <filter>specify_outputs == 'just_calMD' or specify_outputs == 'both'</filter>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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48 </data>
6
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49 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
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b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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50 <filter>specify_outputs == 'calMDandMQ' or specify_outputs == 'both'</filter>
6
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51 </data>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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56 <param name="reference_source_selector" value="history" />
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57 <param name="specify_outputs" value="calMDandMQ" />
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58 <param name="ref_file" value="chr22.fa" />
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59 <output name="fullfilter" file="full.bam" ftype="bam" />
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60 </test>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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61 <test>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
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62 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
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63 <param name="reference_source_selector" value="history" />
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64 <param name="ref_file" value="chr22.fa" />
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65 <param name="specify_outputs" value="both" />
4
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66 <output name="calmd" file="calmd.bam" ftype="bam" />
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67 <output name="fullfilter" file="full.bam" ftype="bam" />
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68 </test>
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69 <test>
7
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70 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
4
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71 <param name="reference_source_selector" value="history" />
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72 <param name="specify_outputs" value="just_calMD" />
7
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73 <param name="ref_file" value="chr22.fa" />
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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74 <output name="calmd" file="calmd.bam" ftype="bam" />
1
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75 </test>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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76 </tests>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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77 <help>
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78 ARTbio bam cleaning overview
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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79 ============================
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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80
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81 .. class:: infomark
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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82
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65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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83 This tool is wrapping several cleaning steps to produce bam files suitable for subsequent
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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84 analyses with lumpy-smoove (or other large structural variation callers) or with
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745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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85 somatic-varscan (or other small structural variation callers)
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65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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86
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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87
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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88 Workflow
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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89 =============
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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90
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91 .. class:: infomark
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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92
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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93 The tool is using the following command line for filtering:
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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94
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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95 ::
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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96
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97 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)' -f 'bam' $input_base".bam"
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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98 &#124; bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
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65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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99 &#124; samtools calmd -C 50 -b -@ 4 - reference.fa &gt; $input_base".filt1.dedup.bamleft.calmd.bam" ;
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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100 sambamba view -h -t 8 --filter='mapping_quality &lt;&#61; 254' -f 'bam' -o $input_base".filt1.dedup.bamleft.calmd.filt2.bam" $input_base".filt1.dedup.bamleft.calmd.bam"
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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101
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102 .. class:: warningmark
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103
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104 From version **1.7+galaxy0**, this tool assumes that the input bam already has its
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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105 optical/PCR duplicate alignments marked appropriately in their flag value. If it is not the
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
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106 case, it may be necessary to use tool that perform this job, for instance samtools markdup,
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107 or sambamba markdup.
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108
0
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109 Purpose
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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110 --------
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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111
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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112 This "workflow" tool was generated in order to limit the number of ``python metadata/set.py`` jobs
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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113 which occur at each step of standard galaxy workflows. Indeed, these jobs are poorly optimized and may last considerable
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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114 amounts of time when datasets are large, at each step, lowering the overall performance of the workflow.
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115
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116 </help>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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117 <citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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118 <citation type="doi">10.1371/journal.pone.0168397</citation>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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119 </citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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120 </tool>