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annotate bwa-mem.xml @ 6:a4d167793afa draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387
author devteam
date Tue, 21 Nov 2017 09:11:06 -0500
parents b59a6178a6e0
children cbc665adcde4
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <?xml version="1.0"?>
5
b59a6178a6e0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d
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2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0">
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <macros>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 <import>read_group_macros.xml</import>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <import>bwa_macros.xml</import>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 </macros>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <expand macro="requirements" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <expand macro="stdio" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <command>
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11 <![CDATA[
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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12 @set_reference_fasta_filename@
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 ## Begin BWA-MEM command line
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 bwa mem
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 -t "\${GALAXY_SLOTS:-1}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 -v 1 ## Verbosity is set to 1 (errors only)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 #if str( $fastq_input.fastq_input_selector ) == "paired_iv": ## For interleaved fastq files set -p option
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 -p
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 -I "${fastq_input.iset_stats}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 #end if
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 #end if
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 #if str( $analysis_type.analysis_type_selector ) == "pacbio":
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 -x pacbio
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b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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29 #elif str( $analysis_type.analysis_type_selector ) == "ont2d":
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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30 -x ont2d
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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31 #elif str( $analysis_type.analysis_type_selector ) == "intractg":
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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32 -x intractg
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 #elif str( $analysis_type.analysis_type_selector ) == "full":
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 -k "${analysis_type.algorithmic_options.k}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 -w "${analysis_type.algorithmic_options.w}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 -d "${analysis_type.algorithmic_options.d}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 -r "${analysis_type.algorithmic_options.r}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 -y "${analysis_type.algorithmic_options.y}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 -c "${analysis_type.algorithmic_options.c}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 -D "${analysis_type.algorithmic_options.D}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 -W "${analysis_type.algorithmic_options.W}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 -m "${analysis_type.algorithmic_options.m}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 ${analysis_type.algorithmic_options.S}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 ${analysis_type.algorithmic_options.P}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 ${analysis_type.algorithmic_options.e}
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47 #end if
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48
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49 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set": ## Scoring options
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50 -A "${analysis_type.scoring_options.A}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51 -B "${analysis_type.scoring_options.B}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 -O "${analysis_type.scoring_options.O}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 -E "${analysis_type.scoring_options.E}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 -L "${analysis_type.scoring_options.L}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 -U "${analysis_type.scoring_options.U}"
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56 #end if
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57
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58 #if str( $analysis_type.io_options.io_options_selector ) == "set": ## IO options
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59 -T "${analysis_type.io_options.T}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60 -h "${analysis_type.io_options.h}"
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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61 ${analysis_type.io_options.a}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 ${analysis_type.io_options.C}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 ${analysis_type.io_options.V}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64 ${analysis_type.io_options.Y}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 ${analysis_type.io_options.M}
5
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66 ${analysis_type.io_options.five}
6
a4d167793afa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387
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67 ${analysis_type.io_options.q}
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 #end if
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69
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70 #end if
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71
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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72 ## Handle read group options...
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 @define_read_group_helpers@
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 #if str( $fastq_input.fastq_input_selector ) == "paired":
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 #else:
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 #end if
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 @set_use_rg_var@
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 @set_read_group_vars@
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 #if $use_rg
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 @set_rg_string@
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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83 -R '$rg_string'
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84 #end if
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85
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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86 #if str( $fastq_input.fastq_input_selector ) == "paired":
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87 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
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88 -I "${fastq_input.iset_stats}"
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89 #end if
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90
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91 "${reference_fasta_filename}"
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92 "${fastq_input.fastq_input1}" "${fastq_input.fastq_input2}"
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93 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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94 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
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95 -I "${fastq_input.iset_stats}"
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96 #end if
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97
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98 "${reference_fasta_filename}"
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99 "${fastq_input.fastq_input1.forward}" "${fastq_input.fastq_input1.reverse}"
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100 #else:
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101 "${reference_fasta_filename}"
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102 "${fastq_input.fastq_input1}"
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103 #end if
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104
2
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105 | samtools sort -O bam -o '$bam_output'
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106 ]]>
0
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107 </command>
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108
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109 <inputs>
2
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110 <expand macro="reference_source_conditional" />
0
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111 <conditional name="fastq_input">
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112 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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113 <option value="paired">Paired</option>
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114 <option value="single">Single</option>
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115 <option value="paired_collection">Paired Collection</option>
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116 <option value="paired_iv">Paired Interleaved</option>
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117 </param>
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118 <when value="paired">
4
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119 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
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120 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
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121 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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122 <sanitizer invalid_char="">
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123 <valid initial="string.digits"><add value=","/> </valid>
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124 </sanitizer>
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125 </param>
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126 </when>
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127 <when value="single">
4
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128 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
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129 </when>
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130 <when value="paired_collection">
4
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131 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
0
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132 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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133 <sanitizer invalid_char="">
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134 <valid initial="string.digits"><add value=","/> </valid>
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135 </sanitizer>
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136 </param>
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137 </when>
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138 <when value="paired_iv">
4
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139 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
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140 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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141 <sanitizer invalid_char="">
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142 <valid initial="string.digits"><add value=","/> </valid>
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143 </sanitizer>
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144 </param>
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145 </when>
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146 </conditional>
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147
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148 <expand macro="read_group_conditional" />
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149
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150 <conditional name="analysis_type">
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151 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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152 <option value="illumina">1.Simple Illumina mode</option>
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153 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
2
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154 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
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155 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
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156 <option value="full">5.Full list of options</option>
0
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157 </param>
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158 <when value="illumina">
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159 <!-- do nothing -->
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160 </when>
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161 <when value="pacbio">
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162 <!-- do nothing. all magic happens within <command> tag -->
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163 </when>
2
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164 <when value="ont2d">
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165 <!-- do nothing. all magic happens within <command> tag -->
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166 </when>
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167 <when value="intractg">
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168 <!-- do nothing. all magic happens within <command> tag -->
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169 </when>
0
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170 <when value="full">
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171 <conditional name="algorithmic_options">
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172 <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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173 <option value="set">Set</option>
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174 <option value="do_not_set" selected="True">Do not set</option>
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175 </param>
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176 <when value="set">
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177 <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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178 <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
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179 <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
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180 <param name="r" type="float" value="1.5" label="Look for internal seeds inside a seed longer than -k * THIS VALUE" help="-r; default=1.5; This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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181 <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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182 <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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183 <param name="D" type="float" value="0.5" label="Drop chains shorter than this fraction of the longest overlapping chain" help="-D; default=0.5"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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184 <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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185 <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
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186 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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187 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
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188 <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
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189 </when>
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190 <when value="do_not_set">
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191 <!-- do nothing -->
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192 </when>
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193 </conditional>
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194
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195 <conditional name="scoring_options">
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196 <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
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197 <option value="set">Set</option>
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198 <option value="do_not_set" selected="True">Do not set</option>
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199 </param>
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200 <when value="set">
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201 <param name="A" type="integer" value="1" label="Score for a sequence match" help="-A; scales options -T, -d, -B, -O, -E, -L, and -U unless overridden; default=1"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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202 <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
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203 <param name="O" type="text" value="6,6" label="Gap open penalties for deletions and insertions" help="-O; default=6,6">
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204 <sanitizer invalid_char="">
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205 <valid initial="string.digits"><add value=","/> </valid>
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206 </sanitizer>
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207 </param>
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208 <param name="E" type="text" value="1,1" label="Gap extension penalties; a gap of size k cost &#39;-O + -E*k&#39;. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=1,1">
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209 <sanitizer invalid_char="">
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210 <valid initial="string.digits"><add value=","/> </valid>
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211 </sanitizer>
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212 </param>
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213 <param name="L" type="text" value="5,5" label="Penalties for 5&#39;-end and 3&#39;-end clipping" help="-L; default=5,5; When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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214 <sanitizer invalid_char="">
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215 <valid initial="string.digits"><add value=","/> </valid>
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216 </sanitizer>
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217 </param>
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218 <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
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219 </when>
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220 <when value="do_not_set">
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221 <!-- do nothing -->
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222 </when>
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223 </conditional>
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224
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225 <conditional name="io_options">
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226 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
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227 <option value="set">Set</option>
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228 <option value="do_not_set" selected="True">Do not set</option>
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229 </param>
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230 <when value="set">
5
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231 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
6
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232 <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
0
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233 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
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234 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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235 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
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236 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
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237 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
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238 <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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239 <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
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240 </when>
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241 <when value="do_not_set">
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242 <!-- do nothing -->
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243 </when>
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244 </conditional>
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245 </when>
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246 </conditional>
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247 </inputs>
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248
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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249 <outputs>
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250 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
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251 <expand macro="dbKeyActionsBwaMem" />
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252 </data>
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253 </outputs>
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254
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255 <tests>
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256 <test>
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257 <param name="reference_source_selector" value="history" />
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258 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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259 <param name="fastq_input_selector" value="paired"/>
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260 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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261 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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262 <param name="analysis_type_selector" value="illumina"/>
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263 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
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264 </test>
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265 <test>
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266 <param name="reference_source_selector" value="history" />
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267 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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268 <param name="fastq_input_selector" value="single"/>
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269 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
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270 <param name="analysis_type_selector" value="illumina"/>
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271 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="2" />
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272 </test>
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273 <test>
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274 <param name="reference_source_selector" value="history" />
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275 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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276 <param name="fastq_input_selector" value="paired"/>
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277 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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278 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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279 <param name="analysis_type_selector" value="illumina"/>
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280 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
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281 </test>
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282 <test>
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283 <param name="reference_source_selector" value="history" />
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284 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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285 <param name="index_a" value="is"/>
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286 <param name="fastq_input_selector" value="paired"/>
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287 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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288 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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289 <param name="rg_selector" value="set"/>
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290 <param name="ID" value="rg1"/>
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291 <param name="PL" value="CAPILLARY"/>
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292 <param name="LB" value="AARDVARK-1" />
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293 <param name="analysis_type_selector" value="illumina"/>
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294 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
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295 </test>
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296 </tests>
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297 <help>
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298 **What is does**
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299
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300 From http://arxiv.org/abs/1303.3997:
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301
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302 BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.
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303 It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
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304 The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
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305 For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date.
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306
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307 It is best suited for mapping long (>70 nt) reads against large reference genomes.
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308
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309 This Galaxy tool wraps bwa-mem module of bwa read mapping tool. Galaxy implementation takes fastq files as input and produces output in BAM (not SAM) format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
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310
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311 -----
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312
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313 **Indices: Selecting reference genomes for BWA**
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314
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315 Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
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316
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317 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
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318 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.
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319
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320 If your genome of interest is not listed here you have two choices:
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321
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322 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
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323 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
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324
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325 -----
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326
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327 **Galaxy-specific option**
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328
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329 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
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330
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331 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem &lt;reference index&gt; &lt;fastq dataset1&gt; [fastq dataset2]
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332 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 &lt;reference index&gt; &lt;PacBio dataset in fastq format&gt;
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333 3. *Full list of options*: Allows access to all options through Galaxy interface.
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334
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335 ------
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336
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337 **BWA MEM options**
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338
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339 Each Galaxy parameter widget corresponds to command line flags listed below:
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340
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341 Algorithm options::
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342
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343 -k INT minimum seed length [19]
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344 -w INT band width for banded alignment [100]
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345 -d INT off-diagonal X-dropoff [100]
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346 -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
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347 -y INT find MEMs longer than {-k} * {-r} with size less than INT [0]
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348 -c INT skip seeds with more than INT occurrences [500]
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349 -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
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350 -W INT discard a chain if seeded bases shorter than INT [0]
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351 -m INT perform at most INT rounds of mate rescues for each read [50]
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352 -S skip mate rescue
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353 -P skip pairing; mate rescue performed unless -S also in use
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354 -e discard full-length exact matches
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355
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356 Scoring options::
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357
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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358 -A INT score for a sequence match, which scales options -TdBOELU unless overridden [1]
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359 -B INT penalty for a mismatch [4]
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360 -O INT[,INT] gap open penalties for deletions and insertions [6,6]
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361 -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]
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362 -L INT[,INT] penalty for 5'- and 3'-end clipping [5,5]
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363 -U INT penalty for an unpaired read pair [17]
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364
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365 Input/output options::
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366
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367 -p first query file consists of interleaved paired-end sequences
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368 -R STR read group header line such as '@RG\tID:foo\tSM:bar' [null]
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369
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370 -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
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371 -T INT minimum score to output [30]
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372 -h INT if there are &lt;INT hits with score &gt;80% of the max score, output all in XA [5]
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373 -a output all alignments for SE or unpaired PE
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374 -C append FASTA/FASTQ comment to SAM output
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375 -V output the reference FASTA header in the XR tag
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376 -Y use soft clipping for supplementary alignments
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377 -M mark shorter split hits as secondary
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378
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379 -I FLOAT[,FLOAT[,INT[,INT]]]
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380 specify the mean, standard deviation (10% of the mean if absent), max
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381 (4 sigma from the mean if absent) and min of the insert size distribution.
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382 FR orientation only. [inferred]
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383
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384 @dataset_collections@
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385
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386 @RG@
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387
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388 @info@
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389 </help>
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390 <citations>
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391 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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392 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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393 <citation type="bibtex">@misc{1303.3997,
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394 Author = {Heng Li},
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395 Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
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396 Year = {2013},
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397 Eprint = {arXiv:1303.3997},
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398 url = {http://arxiv.org/abs/1303.3997},
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399 }</citation>
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400 </citations>
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401 </tool>