Mercurial > repos > iuc > bwa_mem2

annotate bwa-mem2.xml @ 6:9e5466313f1f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit f7942fbad20a3378a95cb84e90ed14c31c192a4f
author iuc
date Thu, 03 Apr 2025 06:50:28 +0000
parents e25b60805367
children
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47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
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1 <tool id="bwa_mem2" name="BWA-MEM2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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2 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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3 <macros>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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4 <import>read_group_macros.xml</import>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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5 <import>macros.xml</import>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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6 </macros>
2
bbb670b70b54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 563c0931e9fc14b0d6e8a7d64ad042a483ec9bb4"
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7 <expand macro="xrefs"/>
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b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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8 <expand macro="requirements">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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9 <requirement type="package" version="1.21">samtools</requirement>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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10 </expand>
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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11 <expand macro="stdio"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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12 <command><![CDATA[
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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13 @pipefail@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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14 @set_reference_fasta_filename@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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16 ## Begin BWA-MEM command line
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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17
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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18 bwa-mem2 mem
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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19 #if str( $output_sort ) == "unsorted":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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20 -t 1
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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21 #else
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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22 -t "\${GALAXY_SLOTS:-1}"
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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23 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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24 ## Verbosity is set to 1 (errors only)
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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25 -v 1
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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27 #if str( $fastq_input.fastq_input_selector ) == "paired_iv":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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28 ## For interleaved fastq files set -p option
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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29 -p
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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30 ## check that insert statistics is used
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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31 #if str( $fastq_input.iset_stats ):
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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32 -I '${fastq_input.iset_stats}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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33 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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34 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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35
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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36 #if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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37 -x '$analysis_type.analysis_type_selector'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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38 #elif str( $analysis_type.analysis_type_selector ) == "full":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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39 ## Algorithmic options
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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40 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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41 -k '${analysis_type.algorithmic_options.k}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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42 -w '${analysis_type.algorithmic_options.w}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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43 -d '${analysis_type.algorithmic_options.d}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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44 -r '${analysis_type.algorithmic_options.r}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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45 -y '${analysis_type.algorithmic_options.y}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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46 -c '${analysis_type.algorithmic_options.c}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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47 -D '${analysis_type.algorithmic_options.D}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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48 -W '${analysis_type.algorithmic_options.W}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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49 -m '${analysis_type.algorithmic_options.m}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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50 ${analysis_type.algorithmic_options.S}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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51 ${analysis_type.algorithmic_options.P}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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52 ${analysis_type.algorithmic_options.e}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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53 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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54
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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55 ## Scoring options
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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56 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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57 -A '${analysis_type.scoring_options.A}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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58 -B '${analysis_type.scoring_options.B}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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59 -O '${analysis_type.scoring_options.O}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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60 -E '${analysis_type.scoring_options.E}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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61 -L '${analysis_type.scoring_options.L}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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62 -U '${analysis_type.scoring_options.U}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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63 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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64
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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65 ## IO options
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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66 #if str( $analysis_type.io_options.io_options_selector ) == "set":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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67 -T '${analysis_type.io_options.T}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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68 -h '${analysis_type.io_options.h}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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69 ${analysis_type.io_options.a}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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70 ${analysis_type.io_options.C}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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71 ${analysis_type.io_options.V}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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72 ${analysis_type.io_options.Y}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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73 ${analysis_type.io_options.M}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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74 ${analysis_type.io_options.five}
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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75 ${analysis_type.io_options.q}
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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76 #if str( $analysis_type.io_options.K ):
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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77 -K '${analysis_type.io_options.K}'
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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78 #end if
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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79 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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80
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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81 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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82
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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83 ## Handle read group options...
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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84 @define_read_group_helpers@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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85 #if str( $fastq_input.fastq_input_selector ) == "paired":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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86 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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87 #else:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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88 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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89 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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90 @set_use_rg_var@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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91 @set_read_group_vars@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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92 #if $use_rg
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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93 @set_rg_string@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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94 -R '$rg_string'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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95 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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96
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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97 #if str( $fastq_input.fastq_input_selector ) == "paired":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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98 ## check that insert statistics is used
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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99 #if str( $fastq_input.iset_stats ):
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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100 -I '${fastq_input.iset_stats}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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101 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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102
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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103 '${reference_fasta_filename}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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104 '${fastq_input.fastq_input1}' '${fastq_input.fastq_input2}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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105 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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106 ## check that insert statistics is used
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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107 #if str( $fastq_input.iset_stats ):
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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108 -I '${fastq_input.iset_stats}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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109 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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110
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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111 '${reference_fasta_filename}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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112 '${fastq_input.fastq_input1.forward}' '${fastq_input.fastq_input1.reverse}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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113 #else:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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114 '${reference_fasta_filename}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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115 '${fastq_input.fastq_input1}'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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116 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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117
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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118 #if str( $output_sort ) == "coordinate":
6
9e5466313f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit f7942fbad20a3378a95cb84e90ed14c31c192a4f
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119 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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120 #elif str( $output_sort ) == "name":
6
9e5466313f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit f7942fbad20a3378a95cb84e90ed14c31c192a4f
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121 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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122 #else
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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123 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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124 #end if
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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125
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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126
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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127 ]]></command>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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128
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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129 <inputs>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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130 <expand macro="reference_source_conditional" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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131 <conditional name="fastq_input">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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132 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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133 <option value="paired">Paired</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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134 <option value="single">Single</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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135 <option value="paired_collection">Paired Collection</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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136 <option value="paired_iv">Paired Interleaved</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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137 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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138 <when value="paired">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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139 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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140 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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141 <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.">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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142 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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143 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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144 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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145 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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146 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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147 <when value="single">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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148 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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149 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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150 <when value="paired_collection">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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151 <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"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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152 <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.">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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153 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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154 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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155 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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156 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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157 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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158 <when value="paired_iv">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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159 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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160 <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.">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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diff changeset
161 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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162 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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163 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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164 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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diff changeset
165 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
166 </conditional>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
167
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
168 <expand macro="read_group_conditional" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
169
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
170 <conditional name="analysis_type">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
171 <param name="analysis_type_selector" type="select" label="Select analysis mode">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
172 <option value="illumina">1.Simple Illumina mode</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
173 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
174 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
175 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
176 <option value="full">5.Full list of options</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
177 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
178 <when value="illumina">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
179 <!-- do nothing -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
180 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
181 <when value="pacbio">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
182 <!-- do nothing. all magic happens within <command> tag -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
183 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
184 <when value="ont2d">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
185 <!-- do nothing. all magic happens within <command> tag -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
186 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
187 <when value="intractg">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
188 <!-- do nothing. all magic happens within <command> tag -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
189 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
190 <when value="full">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
191 <conditional name="algorithmic_options">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
192 <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.">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
193 <option value="set">Set</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
194 <option value="do_not_set" selected="True">Do not set</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
195 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
196 <when value="set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
197 <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
198 <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
199 <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
200 <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" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
201 <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
202 <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
203 <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"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
204 <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
205 <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
206 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
207 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
208 <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
209 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
210 <when value="do_not_set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
211 <!-- do nothing -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
212 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
213 </conditional>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
214
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
215 <conditional name="scoring_options">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
216 <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
217 <option value="set">Set</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
218 <option value="do_not_set" selected="True">Do not set</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
219 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
220 <when value="set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
221 <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"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
222 <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
223 <param name="O" type="text" value="6,6" label="Gap open penalties for deletions and insertions" help="-O; default=6,6">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
224 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
225 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
226 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
227 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
228 <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">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
229 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
230 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
231 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
232 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
233 <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">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
234 <sanitizer invalid_char="">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
235 <valid initial="string.digits"><add value=","/> </valid>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
236 </sanitizer>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
237 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
238 <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
239 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
240 <when value="do_not_set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
241 <!-- do nothing -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
242 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
243 </conditional>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
244
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
245 <conditional name="io_options">
3
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246 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, -M, and -K options.">
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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247 <option value="set">Set</option>
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248 <option value="do_not_set" selected="True">Do not set</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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249 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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250 <when value="set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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251 <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"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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252 <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."/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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253 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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254 <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" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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255 <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"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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256 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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257 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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258 <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" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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259 <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" />
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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260 <param name="K" type="integer" optional="True" label="Process this number of input bases in each batch regardless of nThreads (for reproducibility)" help="-K"/>
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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261 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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262 <when value="do_not_set">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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263 <!-- do nothing -->
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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264 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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265 </conditional>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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266 </when>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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267 </conditional>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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268 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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269 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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270 <option value="name">Sort by read names (i.e., the QNAME field) </option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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271 <option value="unsorted">Not sorted (sorted as input)</option>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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272 </param>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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273 </inputs>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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274
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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275 <outputs>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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276 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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277 <expand macro="dbKeyActionsBwaMem" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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278 <change_format>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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diff changeset
279 <when input="output_sort" value="name" format="qname_sorted.bam" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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280 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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281 </change_format>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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282 </data>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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283 </outputs>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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284
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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285 <tests>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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286 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
287 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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288 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
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289 <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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diff changeset
290 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
291 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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diff changeset
292 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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diff changeset
293 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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diff changeset
294 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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295 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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parents: 3
diff changeset
296 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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297 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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298 </conditional>
3
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iuc
parents: 2
diff changeset
299 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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diff changeset
300 </test>
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iuc
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301 <test>
4
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parents: 3
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302 <conditional name="reference_source">
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303 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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304 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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305 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
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306 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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307 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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308 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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309 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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310 </conditional>
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diff changeset
311 <conditional name="analysis_type">
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312 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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313 </conditional>
3
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314 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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315 </test>
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316 <test>
4
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317 <conditional name="reference_source">
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318 <param name="reference_source_selector" value="history" />
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319 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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320 </conditional>
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iuc
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diff changeset
321 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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diff changeset
322 <param name="fastq_input_selector" value="single"/>
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iuc
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diff changeset
323 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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324 </conditional>
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325 <conditional name="analysis_type">
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326 <param name="analysis_type_selector" value="illumina"/>
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327 </conditional>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
parents: 2
diff changeset
328 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
329 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
330 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
331 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
332 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
333 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
334 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
335 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
336 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
337 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
338 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
339 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
340 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
341 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
342 </conditional>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
parents: 2
diff changeset
343 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
344 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
345 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
346 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
347 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
348 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
349 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
350 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
351 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
352 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
353 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
354 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
355 <conditional name="rg">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
356 <param name="rg_selector" value="set"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
357 <conditional name="read_group_id_conditional">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
358 <param name="ID" value="rg1"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
359 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
360 <conditional name="read_group_lb_conditional">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
361 <param name="LB" value="AARDVARK-1" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
362 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
363 <param name="PL" value="CAPILLARY"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
364 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
365 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
366 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
367 </conditional>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
parents: 2
diff changeset
368 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
369 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
370 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
371 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
372 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
373 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
374 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
375 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
376 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
377 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
378 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
379 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
380 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
381 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
382 </conditional>
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
383 <param name="output_sort" value="unsorted"/>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
parents: 2
diff changeset
384 <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
385 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
386 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
387 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
388 <param name="reference_source_selector" value="history" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
389 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
390 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
391 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
392 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
393 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
394 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
395 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
396 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
397 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
398 </conditional>
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
399 <param name="output_sort" value="name"/>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
iuc
parents: 2
diff changeset
400 <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
401 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
parents:
diff changeset
402 <test>
4
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
403 <conditional name="reference_source">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
404 <param name="reference_source_selector" value="cached" />
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
405 <param name="ref_file" value="mtgenome"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
406 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
407 <conditional name="fastq_input">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
408 <param name="fastq_input_selector" value="paired"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
409 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
410 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
411 </conditional>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
412 <conditional name="analysis_type">
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
iuc
parents: 3
diff changeset
413 <param name="analysis_type_selector" value="illumina"/>
b855f7538222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
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414 </conditional>
3
47195204ebaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
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415 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
0
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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416 </test>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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417 </tests>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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418 <help><![CDATA[
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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419 **What is does**
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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420 BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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421 The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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422
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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423 The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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424
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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425 -----
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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426
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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427 **Indices: Selecting reference genomes for BWA**
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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428
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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429 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:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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430
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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431 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.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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432 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`.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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433
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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434 If your genome of interest is not listed here you have two choices:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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435
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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436 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
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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437 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.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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438
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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439 -----
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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440
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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441 **Galaxy-specific option**
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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442
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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443 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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444
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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445 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 <reference index> <fastq dataset1> [fastq dataset2]
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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446 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 <reference index> <PacBio dataset in fastq format>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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447 3. *Full list of options*: Allows access to all options through Galaxy interface.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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448
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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449 -----
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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450
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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451 **Bam sorting mode**
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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452
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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453 The generated bam files can be sorted according to three criteria: coordinates, names and input order.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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454
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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455 In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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456
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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457 When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field).
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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458
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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459 Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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460
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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461
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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462 @RG@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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463
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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464 @info@
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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465 ]]></help>
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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466 <expand macro="citations" />
f15e2687f9de "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
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467 </tool>