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annotate artbio_bam_cleaning.xml @ 0:65d6d2b554b3 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
author artbio
date Fri, 02 Oct 2020 00:17:33 +0000
parents
children b550841f568b
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65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
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1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy0">
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"
artbio
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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>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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9 <requirement type="package" version="1.6">samtools</requirement>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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10 <requirement type="package" version="0.7.1">sambamba</requirement>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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11 <requirement type="package" version="1.3.2">freebayes</requirement>
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 &&
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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22 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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23 | samtools rmdup - -
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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24 |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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25 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $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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26 sambamba view -h -t 8 --filter='mapping_quality <= 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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27 ]]></command>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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28 <inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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29 <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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30 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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31 </inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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32 <outputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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33 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" from_work_dir="./input.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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34 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" from_work_dir="./input.filt1.dedup.bamleft.calmd.filt2.bam"/>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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35 </outputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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36 <tests>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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37 <test>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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38 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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39 <param name="reference_source_selector" value="history" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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40 <param name="ref_file" value="chr21.fa" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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41 <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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42 <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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43 </test>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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44 </tests>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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45 <help>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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46 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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47 ============================
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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48
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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49 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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50 analyses with lumpy-smoove (or other large structural variation callers) or with
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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51 somatic-varscan (or small structural variation callers)
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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52
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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53
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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54 Workflow
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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55 =============
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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56
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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57 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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58
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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59 ::
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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60
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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61 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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62 &#124; samtools rmdup - -
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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63 &#124;tee $input_base".filt1.dedup.bam" &#124; bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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64 &#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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65 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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66
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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67 Purpose
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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68 --------
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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69
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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70 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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71 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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72 amounts of time when datasets are large, at each step, lowering the overall performance of the workflow.
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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73
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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74 </help>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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75 <citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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76 <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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77 </citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
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78 </tool>