Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 17:69f044db2445 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
author iuc
date Tue, 14 Nov 2017 15:02:02 -0500
parents def46fdb3909
children e0ca9500999b
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def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01">
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2 <description>- map reads against reference genome</description>
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.3.2">bowtie2</requirement>
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8 <requirement type="package" version="1.3.1">samtools</requirement>
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9 </requirements>
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10 <version_command>bowtie2 --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## prepare bowtie2 index
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13 #set index_path = ''
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14 #if str($reference_genome.source) == "history":
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fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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16 ln -s -f '$reference_genome.own_file' genome.fa &&
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17 #set index_path = 'genome'
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18 #else:
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19 #set index_path = $reference_genome.index.fields.path
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20 #end if
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21
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22 ## Link in the input files, so bowtie2 can tell their type
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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24 #set compressed="False"
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25 #set reads_are_fastq = True
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26 #if str($library.type) == 'paired':
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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27 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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28 #set read1 = "input_f.fastq.gz"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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29 #set compressed = "GZ"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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30 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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31 #set read1 = "input_f.fastq.bz2"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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32 #set compressed = "BZ2"
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def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
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33 #else if $library.input_1.is_of_type('fasta'):
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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parents: 15
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34 #set reads_are_fastq = False
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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35 #set read1 = "input_f.fasta"
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36 #else:
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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37 #set read1 = "input_f.fastq"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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38 #end if
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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39 ln -f -s '${library.input_1}' ${read1} &&
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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41 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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42 #set read2 = "input_r.fastq.gz"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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43 #set compressed = "GZ"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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45 #set read2 = "input_r.fastq.bz2"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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46 #set compressed = "BZ2"
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47 #else if $library.input_2.is_of_type('fasta'):
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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48 #set read2 = "input_r.fasta"
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49 #else:
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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50 #set read2 = "input_r.fastq"
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51 #end if
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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52 ln -f -s '${library.input_2}' ${read2} &&
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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53 #else if str($library.type) == 'paired_collection':
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54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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55 #set read1 = "input_f.fastq.gz"
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56 #set compressed = "GZ"
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57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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58 #set read1 = "input_f.fastq.bz2"
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59 #set compressed = "BZ2"
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60 #else if $library.input_1.forward.is_of_type('fasta'):
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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61 #set reads_are_fastq = False
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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62 #set read1 = "input_f.fasta"
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63 #else:
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64 #set read1 = "input_f.fastq"
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65 #end if
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66 ln -s '${library.input_1.forward}' ${read1} &&
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67
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68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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69 #set read2 = "input_r.fastq.gz"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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70 #set compressed = "GZ"
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71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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72 #set read2 = "input_r.fastq.bz2"
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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73 #set compressed = "BZ2"
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74 #else if $library.input_1.reverse.is_of_type("fasta"):
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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75 #set read2 = "input_r.fasta"
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76 #else:
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77 #set read2 = "input_r.fastq"
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78 #end if
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79 ln -s '${library.input_1.reverse}' ${read2} &&
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81 #else if str($library.type) == 'paired_interleaved':
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82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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83 #set read1 = "input_il.fastq.gz"
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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84 #set compressed = "GZ"
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
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85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
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86 #set read1 = "input_il.fastq.bz2"
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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87 #set compressed = "BZ2"
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88 #else if $library.input_1.is_of_type("fasta"):
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89 #set reads_are_fastq = False
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90 #set read1 = "input_il.fasta"
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91 #else:
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92 #set read1 = "input_il.fastq"
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93 #end if
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94 ln -s '${library.input_1}' ${read1} &&
14
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95 #else:
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96 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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97 #set read1 = "input_f.fastq.gz"
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98 #set compressed = "GZ"
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99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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100 #set read1 = "input_f.fastq.bz2"
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101 #set compressed = "BZ2"
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102 #else if $library.input_1.is_of_type("fasta"):
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103 #set reads_are_fastq = False
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104 #set read1 = "input_f.fasta"
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105 #else:
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106 #set read1 = "input_f.fastq"
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107 #end if
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108 ln -s '${library.input_1}' ${read1} &&
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109 #end if
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110
0
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111 ## execute bowtie2
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112
0
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113 bowtie2
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114
0
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115 ## number of threads
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116 -p \${GALAXY_SLOTS:-4}
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117
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118 ## index file path
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119 -x '$index_path'
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120
16
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121 ## Input reads are fasta?
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122 #if not reads_are_fastq:
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123 -f
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124 #end if
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125
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126 ## Input reads
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127 #if str( $library.type ) == "single":
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128 -U '${read1}'
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129 #if str( $library.unaligned_file ) == "true":
14
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130 #if $compressed == "GZ":
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131 --un-gz '${output_unaligned_reads_l}'
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132 #else if $compressed == "BZ2":
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133 --un-bz2 '${output_unaligned_reads_l}'
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134 #else:
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135 --un '${output_unaligned_reads_l}'
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136 #end if
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137 #end if
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138 #if str( $library.aligned_file ) == "true":
14
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139 #if $compressed == "GZ":
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140 --al-gz '${output_aligned_reads_l}'
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141 #else if $compressed == "BZ2":
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142 --al-bz2 '${output_aligned_reads_l}'
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143 #else:
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144 --al '${output_aligned_reads_l}'
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145 #end if
0
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146 #end if
15
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147
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148 #elif str( $library.type ) == "paired_interleaved":
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149 --interleaved '${read1}'
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150 #if str( $library.unaligned_file ) == "true":
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151 #if $compressed == "GZ":
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152 --un-gz '${output_unaligned_reads_l}'
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153 #else if $compressed == "BZ2":
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154 --un-bz2 '${output_unaligned_reads_l}'
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155 #else:
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156 --un '${output_unaligned_reads_l}'
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157 #end if
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158 #end if
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159 #if str( $library.aligned_file ) == "true":
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160 #if $compressed == "GZ":
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161 --al-gz '${output_aligned_reads_l}'
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162 #else if $compressed == "BZ2":
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163 --al-bz2 '${output_aligned_reads_l}'
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164 #else:
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165 --al '${output_aligned_reads_l}'
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166 #end if
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167 #end if
14
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168 #else:
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169 -1 '${read1}'
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170 -2 '${read2}'
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171 #if str( $library.unaligned_file ) == "true":
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172 #if $compressed == "GZ":
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173 --un-conc-gz '${output_unaligned_reads_l}'
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174 #else if $compressed == "BZ2":
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175 --un-conc-bz2 '${output_unaligned_reads_l}'
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176 #else:
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177 --un-conc '${output_unaligned_reads_l}'
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178 #end if
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179 #end if
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180 #if str( $library.aligned_file ) == "true":
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181 #if $compressed == "GZ":
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182 --al-conc-gz '${output_aligned_reads_l}'
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183 #else if $compressed == "BZ2":
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184 --al-conc-bz2 '${output_aligned_reads_l}'
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185 #else:
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186 --al-conc '${output_aligned_reads_l}'
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187 #end if
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188 #end if
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189 #if str( $library.paired_options.paired_options_selector ) == "yes":
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190 -I "${library.paired_options.I}"
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191 -X "${library.paired_options.X}"
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192 ${library.paired_options.fr_rf_ff}
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193 ${library.paired_options.no_mixed}
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194 ${library.paired_options.no_discordant}
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195 ${library.paired_options.dovetail}
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196 ${library.paired_options.no_contain}
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197 ${library.paired_options.no_overlap}
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198 #end if
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199 #end if
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200
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201 ## Read group information.
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202 @define_read_group_helpers@
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203 #if str( $library.type ) == "single":
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204 #set $rg_auto_name = $read_group_name_default($library.input_1)
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205 #elif str( $library.type ) == "paired":
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206 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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207 #else
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208 #set $rg_auto_name = $read_group_name_default($library.input_1)
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209 #end if
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210 @set_use_rg_var@
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211 @set_read_group_vars@
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212 #if $use_rg
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213 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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215 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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216 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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217 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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218 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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219 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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220 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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221 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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222 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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223 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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224 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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225 #end if
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226
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227 ## Analysis type
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228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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229 $analysis_type.presets
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230 #elif str( $analysis_type.analysis_type_selector ) == "full":
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231 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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232 --skip "${analysis_type.input_options.skip}"
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233 --qupto "${analysis_type.input_options.qupto}"
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234 --trim5 "${analysis_type.input_options.trim5}"
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235 --trim3 "${analysis_type.input_options.trim3}"
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236 ${analysis_type.input_options.qv_encoding}
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237 ${analysis_type.input_options.solexa_quals}
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238 ${analysis_type.input_options.int_quals}
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239 #end if
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240
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241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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242 -N "${analysis_type.alignment_options.N}"
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243 -L "${analysis_type.alignment_options.L}"
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244 -i "${analysis_type.alignment_options.i}"
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245 --n-ceil "${analysis_type.alignment_options.n_ceil}"
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246 --dpad "${analysis_type.alignment_options.dpad}"
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247 --gbar "${analysis_type.alignment_options.gbar}"
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248 ${analysis_type.alignment_options.ignore_quals}
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249 ${analysis_type.alignment_options.nofw}
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250 ${analysis_type.alignment_options.norc}
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251 ${analysis_type.alignment_options.no_1mm_upfront}
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252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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253 --end-to-end
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254 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
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255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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256 --local
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257 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
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258 #end if
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259 #end if
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260
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261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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262 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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263 --ma "${analysis_type.scoring_options.ma}"
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264 #end if
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265 --mp "${analysis_type.scoring_options.mp}"
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266 --np "${analysis_type.scoring_options.np}"
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267 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
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268 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
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269 #end if
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270
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271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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272 -k "${analysis_type.reporting_options.k}"
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273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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274 -a
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275 #end if
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276
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277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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278 -D "${analysis_type.effort_options.D}"
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279 -R "${analysis_type.effort_options.R}"
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280 #end if
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281
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282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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283 ${analysis_type.sam_options.no_unal}
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284 ${analysis_type.sam_options.omit_sec_seq}
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285 #end if
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286
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287 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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288 ${analysis_type.other_options.reorder}
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289 ${analysis_type.other_options.non_deterministic}
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290 --seed "${analysis_type.other_options.seed}"
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291 #end if
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292
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293 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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294 ${analysis_type.cline}
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295 #end if
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296
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297 ## mapping stats (i.e. stderr from bowtie2)
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298 #if $save_mapping_stats
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299 2> '$mapping_stats'
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300 #end if
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301
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302 ## output file
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303 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
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304 | samtools sort -O bam -o '$output'
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305 #else
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306 > '$output_sam'
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307 #end if
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308
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309 ## rename unaligned sequence files
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310 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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311 #from os.path import splitext
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312 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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313 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l'
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314 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r'
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315 #end if
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316 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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317 #from os.path import splitext
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318 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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319 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l'
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320 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r'
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321 #end if
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322
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323 ]]></command>
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324 <inputs>
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325 <!-- single/paired -->
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326 <conditional name="library">
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327 <param name="type" type="select" label="Is this single or paired library">
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328 <option value="single">Single-end</option>
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329 <option value="paired">Paired-end</option>
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330 <option value="paired_collection">Paired-end Dataset Collection</option>
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331 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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332 </param>
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333
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334 <when value="single">
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335 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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336
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337 <expand macro="align_unalign" />
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338
0
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339 </when>
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340 <when value="paired">
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341 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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342 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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343
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344 <expand macro="align_unalign" />
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345 <expand macro="paired_end_options" />
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346
2
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347 </when>
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348 <when value="paired_collection">
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349 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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350
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351 <expand macro="align_unalign" />
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352 <expand macro="paired_end_options" />
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353
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354 </when>
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355 <when value="paired_interleaved">
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356 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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357
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358 <expand macro="align_unalign" />
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359 <expand macro="paired_end_options" />
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360
0
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361 </when>
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362 </conditional>
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363
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364 <!-- reference genome -->
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365 <conditional name="reference_genome">
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366 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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367 <option value="indexed">Use a built-in genome index</option>
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368 <option value="history">Use a genome from the history and build index</option>
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369 </param>
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370 <when value="indexed">
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371 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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372 <options from_data_table="bowtie2_indexes">
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373 <filter type="sort_by" column="2"/>
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374 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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375 </options>
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376 </param>
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377 </when>
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378 <when value="history">
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379 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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380 </when>
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381 </conditional>
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382
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383 <!-- read group settings -->
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384 <expand macro="read_group_conditional" />
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385 <conditional name="analysis_type">
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386 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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387 <option value="simple">1: Default setting only</option>
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388 <option value="full">2: Full parameter list</option>
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389 </param>
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390 <when value="simple">
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391 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
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392 <option value="no_presets" selected="True">No, just use defaults</option>
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393 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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394 <option value="--fast">Fast end-to-end (--fast)</option>
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395 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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396 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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397 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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398 <option value="--fast-local">Fast local (--fast-local)</option>
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399 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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400 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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401 </param>
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402 </when>
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403 <when value="full">
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404 <conditional name="input_options">
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405 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
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406 <option value="yes">Yes</option>
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407 <option value="no" selected="true">No</option>
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408 </param>
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409 <when value="yes">
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410 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
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411 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
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412 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
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413 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
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414 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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415 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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416 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
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417 </param>
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418 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
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419 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
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420 </when>
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421 <when value="no">
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422 <!-- do nothing -->
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423 </when>
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424 </conditional>
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425 <conditional name="alignment_options">
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426 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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427 <option value="yes">Yes</option>
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428 <option value="no" selected="true">No</option>
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429 </param>
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430 <when value="yes">
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431 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
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432 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
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433 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
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434 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
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435 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
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436 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
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437 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
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438 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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439 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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440 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
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441 <conditional name="align_mode">
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442 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
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443 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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444 <option value="local">Local (--local)</option>
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445 </param>
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446 <when value="end-to-end">
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447 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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448 </when>
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449 <when value="local">
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450 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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451 </when>
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452 </conditional>
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453 </when>
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454 <when value="no">
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455 <!-- do nothing -->
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456 </when>
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457 </conditional>
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458 <conditional name="scoring_options">
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459 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
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460 <option value="yes">Yes</option>
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461 <option value="no" selected="true">No</option>
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462 </param>
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463 <when value="yes">
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464 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
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465 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
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466 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
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467 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
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468 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
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469 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
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470 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
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471 </when>
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472 <when value="no">
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473 <!-- do nothing -->
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474 </when>
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475 </conditional>
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476 <conditional name="reporting_options">
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477 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
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478 <option value="no" selected="true">No, do not set</option>
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479 <option value="k">Set -k option and enter -k value</option>
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480 <option value="a">Set -a option</option>
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481 </param>
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482 <when value="no">
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483 <!-- do nothing -->
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484 </when>
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485 <when value="k">
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486 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
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487 </when>
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488 <when value="a">
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489 <!-- do nothing here; set -a flag on the command line-->
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490 </when>
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491 </conditional>
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492 <conditional name="effort_options">
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493 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
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494 <option value="yes">Yes</option>
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495 <option value="no" selected="true">No</option>
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496 </param>
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497 <when value="yes">
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498 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
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499 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
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500 </when>
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501 <when value="no">
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502 <!-- do nothing -->
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503 </when>
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504 </conditional>
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505
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506 <conditional name="sam_options">
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507 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
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508 <option value="yes">Yes</option>
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509 <option value="no" selected="true">No</option>
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510 </param>
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511 <when value="yes">
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512 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
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513 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
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514 </when>
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515 <when value="no">
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516 <!-- do nothing -->
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517 </when>
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518 </conditional>
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519 <conditional name="other_options">
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520 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
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521 <option value="yes">Yes</option>
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522 <option value="no" selected="true">No</option>
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523 </param>
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524 <when value="yes">
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525 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
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526 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
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527 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
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528 </when>
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529 <when value="no">
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530 <!-- do nothing -->
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531 </when>
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532 </conditional>
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533 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
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534 </when>
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535 </conditional>
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536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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537 </inputs>
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538
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539 <!-- define outputs -->
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540
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541 <outputs>
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542
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543 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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544 <filter>library['unaligned_file'] is True</filter>
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545 <actions>
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546 <conditional name="library.type">
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547 <when value="single">
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548 <action type="format">
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549 <option type="from_param" name="library.input_1" param_attribute="ext" />
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550 </action>
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551 </when>
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552 <when value="paired">
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553 <action type="format">
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554 <option type="from_param" name="library.input_1" param_attribute="ext" />
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555 </action>
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556 </when>
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557 <when value="paired_collection">
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558 <action type="format">
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559 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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560 </action>
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561 </when>
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562 </conditional>
0
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563 </actions>
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564 </data>
11
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565 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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566 <filter>library['aligned_file'] is True</filter>
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567 <actions>
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568 <conditional name="library.type">
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569 <when value="single">
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570 <action type="format">
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571 <option type="from_param" name="library.input_1" param_attribute="ext" />
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572 </action>
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573 </when>
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574 <when value="paired">
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575 <action type="format">
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576 <option type="from_param" name="library.input_1" param_attribute="ext" />
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577 </action>
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578 </when>
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579 <when value="paired_collection">
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580 <action type="format">
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581 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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582 </action>
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583 </when>
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584 </conditional>
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585 </actions>
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586 </data>
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587 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
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588 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
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589 <actions>
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590 <conditional name="library.type">
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591 <when value="paired">
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592 <action type="format">
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593 <option type="from_param" name="library.input_2" param_attribute="ext" />
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594 </action>
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595 </when>
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596 <when value="paired_collection">
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597 <action type="format">
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598 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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599 </action>
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600 </when>
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601 </conditional>
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602 </actions>
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603 </data>
0
a03a7ee6cdff Imported from capsule None
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604 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
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parents: 1
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605 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
a03a7ee6cdff Imported from capsule None
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606 <actions>
5
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607 <conditional name="library.type">
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608 <when value="paired">
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609 <action type="format">
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610 <option type="from_param" name="library.input_2" param_attribute="ext" />
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611 </action>
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612 </when>
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613 <when value="paired_collection">
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614 <action type="format">
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615 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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616 </action>
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617 </when>
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618 </conditional>
0
a03a7ee6cdff Imported from capsule None
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619 </actions>
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620 </data>
11
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621
5
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622 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
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623 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
0
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624 <actions>
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625 <conditional name="reference_genome.source">
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626 <when value="indexed">
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627 <action type="metadata" name="dbkey">
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628 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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629 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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630 <filter type="param_value" ref="reference_genome.index" column="0"/>
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631 </option>
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632 </action>
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633 </when>
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634 <when value="history">
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635 <action type="metadata" name="dbkey">
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636 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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637 </action>
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638 </when>
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639 </conditional>
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640 </actions>
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641 </data>
5
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642
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643 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
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644 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
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645 <actions>
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646 <conditional name="reference_genome.source">
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647 <when value="indexed">
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648 <action type="metadata" name="dbkey">
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649 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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650 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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651 <filter type="param_value" ref="reference_genome.index" column="0"/>
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652 </option>
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653 </action>
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654 </when>
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655 <when value="history">
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parents: 2
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656 <action type="metadata" name="dbkey">
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657 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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658 </action>
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659 </when>
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660 </conditional>
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661 </actions>
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662 </data>
10
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663 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
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664 <filter>save_mapping_stats is True</filter>
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665 </data>
5
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666
0
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667 </outputs>
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668
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669 <tests>
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670 <test>
17
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671 <!-- test on paired-end datasets -->
2
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672 <param name="type" value="paired"/>
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673 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
674 <param name="unaligned_file" value="false"/>
2
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diff changeset
675 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
676 <param name="source" value="history" />
2
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diff changeset
677 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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parents: 1
diff changeset
678 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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parents: 1
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679 <param name="own_file" value="bowtie2-ref.fasta" />
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devteam
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680 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
681 </test>
5
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diff changeset
682 <test>
17
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iuc
parents: 16
diff changeset
683 <!-- test on paired collection -->
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
684 <param name="type" value="paired_collection"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
685 <param name="paired_options_selector" value="no"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <param name="unaligned_file" value="false"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <param name="analysis_type_selector" value="simple"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
688 <param name="source" value="history" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
689 <param name="input_1">
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diff changeset
690 <collection type="paired">
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
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diff changeset
691 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
692 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
693 </collection>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
694 </param>
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iuc
parents: 16
diff changeset
695 <param name="own_file" value="bowtie2-ref.fasta" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
696 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
697 </test>
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iuc
parents: 16
diff changeset
698 <test>
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iuc
parents: 16
diff changeset
699 <!-- test on paired-end datasets with read group info -->
5
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parents: 2
diff changeset
700 <param name="type" value="paired"/>
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parents: 2
diff changeset
701 <param name="paired_options_selector" value="no"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
702 <param name="unaligned_file" value="false"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
703 <param name="analysis_type_selector" value="simple"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
704 <param name="rg_selector" value="set"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
705 <param name="ID" value="rg1"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
706 <param name="PL" value="CAPILLARY"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
707 <param name="source" value="history" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
708 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
709 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
710 <param name="own_file" value="bowtie2-ref.fasta" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
711 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
712 </test>
10
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devteam
parents: 8
diff changeset
713 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
714 <!-- test on paired-end datasets with stats output -->
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
715 <param name="type" value="paired"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
716 <param name="paired_options_selector" value="no"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
717 <param name="unaligned_file" value="false"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
718 <param name="analysis_type_selector" value="simple"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
719 <param name="source" value="history" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
720 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
721 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
722 <param name="own_file" value="bowtie2-ref.fasta" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
723 <param name="save_mapping_stats" value="true" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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parents: 8
diff changeset
724 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
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iuc
parents: 14
diff changeset
725 <output name="mapping_stats">
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <has_text text="of these" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
728 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
729 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 </test>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
731 <test>
17
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iuc
parents: 16
diff changeset
732 <!-- test on interleaved dataset -->
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
733 <param name="type" value="paired_interleaved"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
734 <!-- <param name="paired_options_selector" value="no"/> -->
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
735 <param name="unaligned_file" value="false"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
736 <param name="analysis_type_selector" value="simple"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
737 <param name="rg_selector" value="set"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
738 <param name="ID" value="rg1"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
739 <param name="PL" value="CAPILLARY"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
740 <param name="source" value="history" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
741 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
742 <param name="own_file" value="bowtie2-ref.fasta" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
743 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
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parents: 8
diff changeset
744 </test>
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parents: 13
diff changeset
745 <test>
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parents: 16
diff changeset
746 <!-- test on fastqsanger.gz paired-end datasets -->
14
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parents: 13
diff changeset
747 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
748 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
749 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
750 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
751 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
752 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
754 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
755 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
756 </test>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
757 <test>
17
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iuc
parents: 16
diff changeset
758 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
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parents: 13
diff changeset
759 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
760 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
761 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
762 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
763 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
764 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
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765 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
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diff changeset
766 <param name="own_file" value="bowtie2-ref.fasta" />
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767 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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768 </test>
16
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diff changeset
769 <test>
17
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diff changeset
770 <!-- test on fasta paired-end datasets -->
16
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diff changeset
771 <param name="type" value="paired"/>
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diff changeset
772 <param name="paired_options_selector" value="no"/>
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diff changeset
773 <param name="unaligned_file" value="false"/>
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diff changeset
774 <param name="analysis_type_selector" value="simple"/>
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diff changeset
775 <param name="source" value="history" />
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diff changeset
776 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
777 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
778 <param name="own_file" value="bowtie2-ref.fasta" />
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779 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
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780 </test>
0
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781 </tests>
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782
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783 <help><![CDATA[
0
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784 **Bowtie2 Overview**
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785
2
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786 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
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787 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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788
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789 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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790 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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791 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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792
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793 -----
0
a03a7ee6cdff Imported from capsule None
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794
2
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795 **Selecting reference genomes for Bowtie2**
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796
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797 Galaxy wrapper for Bowtie2 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:
0
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798
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799 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 bowtie2-build utility and are ready to be mapped against.
2
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800 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 bowtie2-build command, and then run mapping with bowtie2.
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801
2
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802 If your genome of interest is not listed here you have two choices:
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803
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804 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
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805 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
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806
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807 ------
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808
2
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809 .. class:: infomark
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810
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811 **Bowtie2 options**
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812
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813 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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814
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815 -----
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816
0
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817 **Inputs**
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818
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819 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
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820
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821 ------
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822
2
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823 **Input options**::
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824
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825 --interleaved
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826 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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827
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828 -s/--skip <int>
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829 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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830
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831 -u/--qupto <int>
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832 Align the first `<int>` reads or read pairs from the input (after the
2
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833 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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834
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835 -5/--trim5 <int>
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836 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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837
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838 -3/--trim3 <int>
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839 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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840
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841 --phred33
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842 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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843 also called the "Phred+33" encoding, which is used by the very latest Illumina
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844 pipelines.
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845
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846 --phred64
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847 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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848 also called the "Phred+64" encoding.
0
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849
2
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850 --solexa-quals
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851 Convert input qualities from Solexa Phred quality (which can be negative) to
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852 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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853 Pipeline versions (prior to 1.3). Default: off.
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854
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855 --int-quals
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856 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
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857 Integers are treated as being on the Phred quality scale unless
2
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858 `--solexa-quals` is also specified. Default: off.
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859
2
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860 ------
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861
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862 **Presets in `--end-to-end` mode**::
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863
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864 --very-fast
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865 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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866
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867 --fast
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868 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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869
2
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870 --sensitive
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871 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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872
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873 --very-sensitive
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874 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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875
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876 ------
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877
2
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878 **Presets options in `--local` mode**::
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879
2
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880 --very-fast-local
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881 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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882
2
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883 --fast-local
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884 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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885
2
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886 --sensitive-local
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887 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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888
2
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889 --very-sensitive-local
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890 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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891
0
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892 ------
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893
2
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894 **Alignment options**::
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895
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diff changeset
896 -N <int>
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897 Sets the number of mismatches to allowed in a seed alignment during multiseed
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diff changeset
898 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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899 (often much slower) but increases sensitivity. Default: 0.
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900
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901 -L <int>
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902 Sets the length of the seed substrings to align during multiseed alignment.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
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903 Smaller values make alignment slower but more sensitive. Default: the
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diff changeset
904 `--sensitive` preset is used by default, which sets `-L` to 22 in
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
905 `--end-to-end` mode and to 20 in `--local` mode.
2
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906
11
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diff changeset
907 -i <func>
2
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908 Sets a function governing the interval between seed substrings to use during
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
909 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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910 length is 10, and the seed interval is 6, the seeds extracted will be:
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911
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912 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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913 Seed 1 fw: TAGCTACGCT
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914 Seed 1 rc: AGCGTAGCTA
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915 Seed 2 fw: CGCTCTACGC
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916 Seed 2 rc: GCGTAGAGCG
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917 Seed 3 fw: ACGCTATCAT
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918 Seed 3 rc: ATGATAGCGT
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919 Seed 4 fw: TCATGCATAA
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920 Seed 4 rc: TTATGCATGA
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921
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922 Since it's best to use longer intervals for longer reads, this parameter sets
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923 the interval as a function of the read length, rather than a single
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924 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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925 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
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diff changeset
926 If the function returns a result less than
2
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927 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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928 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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929 in `--local` mode.
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930
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diff changeset
931 --n-ceil <func>
2
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932 Sets a function governing the maximum number of ambiguous characters (usually
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933 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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934 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
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935 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
936 Default: `L,0,0.15`.
2
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937
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diff changeset
938 --dpad <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
939 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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940 gaps. Default: 15.
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941
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diff changeset
942 --gbar <int>
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943 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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944 Default: 4.
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945
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946 --ignore-quals
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947 When calculating a mismatch penalty, always consider the quality value at the
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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948 mismatched position to be the highest possible, regardless of the actual value.
2
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949 I.e. input is treated as though all quality values are high. This is also the
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950 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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951 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
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952
2
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953 --nofw/--norc
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954 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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955 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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956 not attempt to align unpaired reads against the reverse-complement (Crick)
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957 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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958 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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959 paired-end configurations corresponding to fragments from the reverse-complement
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960 (Crick) strand. Default: both strands enabled.
2
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961
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962 --no-1mm-upfront
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963 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
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964 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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965 alignments can be found very quickly, and many short read alignments have exact or
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966 near-exact end-to-end alignments. However, this can lead to unexpected
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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967 alignments when the user also sets options governing the multiseed heuristic,
2
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968 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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969 to the length of the read, the user will be surprised to find 1-mismatch alignments
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970 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
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971 alignments before using the multiseed heuristic, which leads to the expected
2
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972 behavior when combined with options such as `-L` and `-N`. This comes at the
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973 expense of speed.
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974
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975 --end-to-end
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976 In this mode, Bowtie 2 requires that the entire read align from one end to the
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977 other, without any trimming (or "soft clipping") of characters from either end.
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978 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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979 are less than or equal to 0, and the greatest possible alignment score is 0.
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980 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
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981
2
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982 --local
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983 In this mode, Bowtie 2 does not require that the entire read align from one end
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984 to the other. Rather, some characters may be omitted ("soft clipped") from the
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985 ends in order to achieve the greatest possible alignment score. The match bonus
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986 `--ma` is used in this mode, and the best possible alignment score is equal to
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987 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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988 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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989 the local version of the preset (`--very-fast-local`). This is mutually
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990 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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991
2
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992 -----
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993
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994 **Scoring options**::
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995
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996 --ma <int>
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997 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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998 score for each position where a read character aligns to a reference character
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999 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1000
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1001 --mp MX,MN
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1002 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1003 number less than or equal to `MX` and greater than or equal to `MN` is
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1004 subtracted from the alignment score for each position where a read character
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1005 aligns to a reference character, the characters do not match, and neither is an
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1006 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1007 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1008 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1009
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1010 --np <int>
2
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1011 Sets penalty for positions where the read, reference, or both, contain an
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1012 ambiguous character such as `N`. Default: 1.
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1013
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1014 --rdg <int1>,<int2>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1015 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1016 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1017
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1018 --rfg <int1>,<int2>
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1019 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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1020 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1021 5, 3.
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a03a7ee6cdff Imported from capsule None
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1022
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1023 --score-min <func>
2
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1024 Sets a function governing the minimum alignment score needed for an alignment to
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1025 be considered "valid" (i.e. good enough to report). This is a function of read
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1026 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
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1027 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and
2
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1028 the default in `--local` mode is `G,20,8`.
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1029
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1030 -----
2
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1031
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1032 **Reporting options**::
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1033
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1034 -k <int>
2
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1035 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1036 When it finds a valid alignment, it continues looking for alignments that are
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1037 nearly as good or better. The best alignment found is reported (randomly
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1038 selected from among best if tied). Information about the best alignments is
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1039 used to estimate mapping quality and to set SAM optional fields, such as
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1040 `AS:i` and `XS:i`.
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1041
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1042 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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1043 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1044 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
1045 finds `<int>`, whichever happens first. All alignments found are reported in
2
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diff changeset
1046 descending order by alignment score. The alignment score for a paired-end
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diff changeset
1047 alignment equals the sum of the alignment scores of the individual mates. Each
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diff changeset
1048 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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parents: 1
diff changeset
1049 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1050 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1051 `<int>` alignments reported are the best possible in terms of alignment score.
2
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diff changeset
1052 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1053
2
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diff changeset
1054 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1055 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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diff changeset
1056
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diff changeset
1057 -a
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diff changeset
1058 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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diff changeset
1059 is mutually exclusive with `-k`.
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diff changeset
1060
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1061 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
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diff changeset
1062 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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diff changeset
1063
2
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diff changeset
1064 -----
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diff changeset
1065
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diff changeset
1066 **Effort options**::
2a6cfe8997aa Uploaded from GH
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diff changeset
1067
11
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diff changeset
1068 -D <int>
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diff changeset
1069 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1070 moves on, using the alignments found so far. A seed extension "fails" if it
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1071 does not yield a new best or a new second-best alignment. This limit is
2a6cfe8997aa Uploaded from GH
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1072 automatically adjusted up when -k or -a are specified. Default: 15.
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diff changeset
1073
11
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diff changeset
1074 -R <int>
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diff changeset
1075 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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diff changeset
1076 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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diff changeset
1077 (same length, same number of mismatches allowed) at different offsets and
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1078 searches for more alignments. A read is considered to have repetitive seeds if
2a6cfe8997aa Uploaded from GH
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1079 the total number of seed hits divided by the number of seeds that aligned at
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1080 least once is greater than 300. Default: 2.
11
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diff changeset
1081
2
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diff changeset
1082 -----
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diff changeset
1083
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diff changeset
1084 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
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1085
11
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diff changeset
1086 -I/--minins <int>
2
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1087 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
2a6cfe8997aa Uploaded from GH
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parents: 1
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1088 specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
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diff changeset
1089 appropriate orientation with a 20-bp gap between them, that alignment is
2a6cfe8997aa Uploaded from GH
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1090 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
2a6cfe8997aa Uploaded from GH
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parents: 1
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1091 be valid in that case. If trimming options `-3` or `-5` are also used, the
2a6cfe8997aa Uploaded from GH
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diff changeset
1092 `-I` constraint is applied with respect to the untrimmed mates.
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diff changeset
1093
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diff changeset
1094 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
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diff changeset
1095 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1096 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1097 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1098 efficient.
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1099
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1100 Default: 0 (essentially imposing no minimum)
2
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1101
11
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diff changeset
1102 -X/--maxins <int>
2
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diff changeset
1103 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1104 is specified and a paired-end alignment consists of two 20-bp alignments in the
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1105 proper orientation with a 60-bp gap between them, that alignment is considered
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1106 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
1107 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1108 constraint is applied with respect to the untrimmed mates, not the trimmed
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1109 mates.
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diff changeset
1110
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1111 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1112 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1113 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1114 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1115 efficient.
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1116
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1117 Default: 500.
0
a03a7ee6cdff Imported from capsule None
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1118
2
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1119 --fr/--rf/--ff
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1120 The upstream/downstream mate orientations for a valid paired-end alignment
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1121 against the forward reference strand. E.g., if `--fr` is specified and there is
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1122 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1123 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1124 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1125 complement of mate 1 and all other constraints are met, that too is valid.
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1126 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1127 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1128 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1129 for Illumina's Paired-end Sequencing Assay).
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1130
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1131 --no-mixed
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1132 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1133 a pair, it then tries to find alignments for the individual mates. This option
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1134 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1135
2
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1136 --no-discordant
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1137 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1138 concordant alignments. A discordant alignment is an alignment where both mates
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diff changeset
1139 align uniquely, but that does not satisfy the paired-end constraints
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1140 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1141
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1142 --dovetail
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1143 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
1144 beginning of the other such that the wrong mate begins upstream, consider that
5
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diff changeset
1145 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1146
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1147 --no-contain
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1148 If one mate alignment contains the other, consider that to be non-concordant.
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1149 Default: a mate can contain the other in a concordant alignment.
2
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1150
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1151 --no-overlap
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1152 If one mate alignment overlaps the other at all, consider that to be
5
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diff changeset
1153 non-concordant. Default: mates can overlap in a concordant alignment.
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1154
0
a03a7ee6cdff Imported from capsule None
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1155 ------
a03a7ee6cdff Imported from capsule None
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1156
2
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1157 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
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1158
11
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1159 --rg-id <text>
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1160 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1161 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1162 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1163 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1164
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diff changeset
1165 --rg <text>
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1166 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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1167 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
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diff changeset
1168 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1169 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1170 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
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1171
2
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diff changeset
1172 --omit-sec-seq
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1173 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1174 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1175 in those fields instead.
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1176
2
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1177 -----
0
a03a7ee6cdff Imported from capsule None
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1178
2
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1179 **Other options**::
0
a03a7ee6cdff Imported from capsule None
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1180
2
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1181 --reorder
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1182 Guarantees that output SAM records are printed in an order corresponding to the
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1183 order of the reads in the original input file, even when `-p` is set greater
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1184 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1185 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1186 not specified. Has no effect if `-p` is set to 1, since output order will
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1187 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
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1188
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diff changeset
1189 --seed <int>
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1190 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
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1191
2
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diff changeset
1192 --non-deterministic
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1193 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1194 seeds the generator with a number derived from (a) the read name, (b) the
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1195 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1196 option. This means that if two reads are identical (same name, same
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diff changeset
1197 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
2a6cfe8997aa Uploaded from GH
devteam
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diff changeset
1198 for both, even if there was ambiguity. When `--non-deterministic` is specified,
2a6cfe8997aa Uploaded from GH
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diff changeset
1199 Bowtie 2 re-initializes its pseudo-random generator for each read using the
2a6cfe8997aa Uploaded from GH
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diff changeset
1200 current time. This means that Bowtie 2 will not necessarily report the same
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1201 alignment for two identical reads. This is counter-intuitive for some users,
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1202 but might be more appropriate in situations where the input consists of many
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1203 identical reads.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1204
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1205 -----
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1206
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1207
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1208 **Paired-end (and mate-pair) data in fastq format**
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1209
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1210 Paired end datasets can be represented as two individual datasets:
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1211
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1212 First dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1213
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1214 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1215 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1216 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1217 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1218 @2/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1219 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1220 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1221 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1222
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1223 Second dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1224
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1225 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1226 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1227 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1228 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1229 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1230 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1231 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1232 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1233
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1234 Or a single *interleaved* dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1235
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1236 @1/1
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parents: 14
diff changeset
1237 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1238 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1239 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1240 @1/2
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parents: 14
diff changeset
1241 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1242 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1243 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1244 @2/1
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parents: 14
diff changeset
1245 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1246 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1247 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1248 @2/2
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parents: 14
diff changeset
1249 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1250 +
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diff changeset
1251 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1252 ]]></help>
2
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1253 <citations>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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parents: 16
diff changeset
1254 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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parents: 16
diff changeset
1255 <citation type="doi">10.1038/nmeth.1923</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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parents: 16
diff changeset
1256 </citations>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1257 </tool>