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annotate bwameth.xml @ 4:95219305823a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:07:16 -0500
parents a6ea26c1f225
children 29bdbc353f20
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95219305823a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
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1 <tool id="bwameth" name="bwameth" version="0.2.0.4" profile="17.01">
0
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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2 <description>Fast and accurate aligner of BS-Seq reads.</description>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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3 <requirements>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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4 <requirement type="package" version="0.2.0">bwameth</requirement>
4
95219305823a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
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5 <requirement type="package" version="0.7.16">bwa</requirement>
0
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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6 </requirements>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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7 <version_command>bwameth.py --version</version_command>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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8 <command detect_errors="aggressive">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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9 <![CDATA[
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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10 #if $referenceSource.source != "indexed":
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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11 mkdir index_dir &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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12 ln -s '$referenceSource.reference' index_dir/genome.fa &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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13 bwameth.py index index_dir/genome.fa &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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14 #set index="index_dir/genome.fa"
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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15 #else
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16 #set index=$referenceSource.index.fields.path
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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17 #end if
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18
3
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19 ## Link in the files with a name that's appropriate
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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20 #if str($single_or_paired.single_or_paired_opts) == 'paired':
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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21 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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22 #set read1 = "input_f.fastq.gz"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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23 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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24 #set read1 = "input_f.fastq.bz2"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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25 #else:
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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26 #set read1 = "input_f.fastq"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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27 #end if
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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28 ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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29
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30 #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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31 #set read2 = "input_r.fastq.gz"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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32 #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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33 #set read2 = "input_r.fastq.bz2"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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34 #else:
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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35 #set read2 = "input_r.fastq"
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36 #end if
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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37 ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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38 #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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39 #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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40 #set read1 = "input_f.fastq.gz"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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41 #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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42 #set read1 = "input_f.fastq.bz2"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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43 #else:
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44 #set read1 = "input_f.fastq"
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45 #end if
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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46 ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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47
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48 #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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49 #set read2 = "input_r.fastq.gz"
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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50 #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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51 #set read2 = "input_r.fastq.bz2"
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52 #else:
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53 #set read2 = "input_r.fastq"
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54 #end if
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55 ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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56 #else:
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57 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
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58 #set read1 = "input_f.fastq.gz"
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59 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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60 #set read1 = "input_f.fastq.bz2"
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61 #else:
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62 #set read1 = "input_f.fastq"
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63 #end if
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64 ln -f -s '${single_or_paired.input_singles}' ${read1} &&
a6ea26c1f225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
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65 #end if
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66
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67
0
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68 bwameth.py
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69 -t "\${GALAXY_SLOTS:-4}"
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70 --reference "${index}"
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71
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72 #if str($readGroup).strip() != "":
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73 --read-group "${readGroup}"
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74 #end if
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75
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76 #if $single_or_paired.single_or_paired_opts == 'single':
3
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77 $read1
0
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78 #else:
3
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79 $read1 $read2
0
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80 #end if
2
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81 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
0
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82 ]]>
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83 </command>
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84 <inputs>
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85 <conditional name="referenceSource">
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86 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
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87 <option value="history" selected="True">Use one from the history</option>
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88 <option value="indexed">Use a built-in index</option>
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89 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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90 <when value="history">
1
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91 <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" />
0
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92 </when>
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93 <when value="indexed">
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94 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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95 <options from_data_table="bwameth_indexes">
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96 <filter type="sort_by" column="2"/>
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97 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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98 </options>
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99 </param>
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100 </when>
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101 </conditional>
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102
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103 <conditional name="single_or_paired">
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104 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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105 <option value="single">Single-end</option>
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106 <option value="paired">Paired-end</option>
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107 <option value="paired_collection">Paired-end Dataset Collection</option>
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108 </param>
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109 <when value="single">
3
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110 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." />
0
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111 </when>
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112 <when value="paired">
3
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113 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." />
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114 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." />
0
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115 </when>
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116 <when value="paired_collection">
3
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117 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
0
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118 </when>
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119 </conditional>
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120 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
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121 <sanitizer sanitize="False"/>
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122 </param>
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123 </inputs>
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124 <outputs>
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125 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
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126 </outputs>
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127 <tests>
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128 <test>
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129 <param name="referenceSource" value="history" />
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130 <param name="reference" value="ref.fa.gz" />
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131 <param name="single_or_paired_opts" value="paired" />
3
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132 <param name="input_mate1" value="t_R1.fastq.gz"/>
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133 <param name="input_mate2" value="t_R2.fastq.gz"/>
0
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134 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
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135 </test>
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136 <test>
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137 <param name="referenceSource" value="history" />
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138 <param name="reference" value="ref.fa.gz" />
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139 <param name="single_or_paired_opts" value="paired_collection" />
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140 <param name="input_mate1">
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141 <collection type="paired">
3
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142 <element name="forward" value="t_R1.fastq.gz"/>
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143 <element name="reverse" value="t_R2.fastq.gz"/>
0
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144 </collection>
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145 </param>
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146 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
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147 </test>
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148 </tests>
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149 <help>
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150 <![CDATA[
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151
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152 **What it does**
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153
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154 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
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155 ]]>
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156 </help>
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157 <citations>
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158 <citation type="bibtex">@misc{1401.1129,
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159 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
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160 Title = {Fast and accurate alignment of long bisulfite-seq reads},
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161 Year = {2014},
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162 Eprint = {arXiv:1401.1129},
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163 }</citation>
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164 </citations>
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165 </tool>