Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 30:2f3400246bfc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
author iuc
date Mon, 31 Jan 2022 08:31:13 +0000
parents 56dcf3929d02
children f66e4858ca26
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8681e741a037 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
iuc
parents: 27
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1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
2
2a6cfe8997aa Uploaded from GH
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2 <description>- map reads against reference genome</description>
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56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <xrefs>
56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <xref type="bio.tools">bowtie2</xref>
56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
5
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6 <macros>
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7 <import>bowtie2_macros.xml</import>
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8 </macros>
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9 <requirements>
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c9105910063f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
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10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
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2f3400246bfc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
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11 <requirement type="package" version="1.14">samtools</requirement>
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12 </requirements>
0
a03a7ee6cdff Imported from capsule None
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13 <version_command>bowtie2 --version</version_command>
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14 <command detect_errors="exit_code"><![CDATA[
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e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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15 ## Use pipefail if available to quit with first non-zero exit code
e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
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16 set -o | grep -q pipefail && set -o pipefail;
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17 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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18 #set index_path = ''
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iuc
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19 #if str($reference_genome.source) == "history":
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20 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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21 ln -s -f '$reference_genome.own_file' genome.fa &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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22 #set index_path = 'genome'
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23 #else:
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24 #set index_path = $reference_genome.index.fields.path
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25 #end if
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27 ## Link in the input files, so bowtie2 can tell their type
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29 #set compressed="False"
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30 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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31 #if str($library.type) == 'paired':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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32 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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33 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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34 #set compressed = "GZ"
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35 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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37 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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38 #else if $library.input_1.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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39 #set reads_are_fastq = False
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40 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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42 #set read1 = "input_f.fastq"
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43 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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44 ln -f -s '${library.input_1}' ${read1} &&
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45
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46 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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47 #set read2 = "input_r.fastq.gz"
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48 #set compressed = "GZ"
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49 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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50 #set read2 = "input_r.fastq.bz2"
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51 #set compressed = "BZ2"
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52 #else if $library.input_2.is_of_type('fasta'):
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53 #set read2 = "input_r.fasta"
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54 #else:
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55 #set read2 = "input_r.fastq"
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56 #end if
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57 ln -f -s '${library.input_2}' ${read2} &&
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58 #else if str($library.type) == 'paired_collection':
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59 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 #set read1 = "input_f.fastq.gz"
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61 #set compressed = "GZ"
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62 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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63 #set read1 = "input_f.fastq.bz2"
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64 #set compressed = "BZ2"
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65 #else if $library.input_1.forward.is_of_type('fasta'):
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66 #set reads_are_fastq = False
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67 #set read1 = "input_f.fasta"
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68 #else:
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69 #set read1 = "input_f.fastq"
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70 #end if
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71 ln -s '${library.input_1.forward}' ${read1} &&
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73 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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74 #set read2 = "input_r.fastq.gz"
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75 #set compressed = "GZ"
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76 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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77 #set read2 = "input_r.fastq.bz2"
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78 #set compressed = "BZ2"
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79 #else if $library.input_1.reverse.is_of_type("fasta"):
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80 #set read2 = "input_r.fasta"
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81 #else:
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82 #set read2 = "input_r.fastq"
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83 #end if
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84 ln -s '${library.input_1.reverse}' ${read2} &&
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85
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86 #else if str($library.type) == 'paired_interleaved':
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87 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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88 #set read1 = "input_il.fastq.gz"
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89 #set compressed = "GZ"
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90 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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91 #set read1 = "input_il.fastq.bz2"
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92 #set compressed = "BZ2"
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93 #else if $library.input_1.is_of_type("fasta"):
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94 #set reads_are_fastq = False
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95 #set read1 = "input_il.fasta"
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96 #else:
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97 #set read1 = "input_il.fastq"
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98 #end if
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99 ln -s '${library.input_1}' ${read1} &&
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100 #else:
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101 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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102 #set read1 = "input_f.fastq.gz"
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103 #set compressed = "GZ"
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104 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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iuc
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105 #set read1 = "input_f.fastq.bz2"
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106 #set compressed = "BZ2"
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107 #else if $library.input_1.is_of_type("fasta"):
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108 #set reads_are_fastq = False
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109 #set read1 = "input_f.fasta"
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110 #else:
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111 #set read1 = "input_f.fastq"
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112 #end if
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113 ln -s '${library.input_1}' ${read1} &&
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114 #end if
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115
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116 ## execute bowtie2
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117
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118 bowtie2
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119
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120 ## number of threads
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121 -p \${GALAXY_SLOTS:-4}
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122
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123 ## index file path
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124 -x '$index_path'
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125
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126 ## Input reads are fasta?
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127 #if not reads_are_fastq:
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128 -f
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129 #end if
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130
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131 ## Input reads
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132 #if str( $library.type ) == "single":
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133 -U '${read1}'
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134 #if str( $library.unaligned_file ) == "true":
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135 #if $compressed == "GZ":
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136 --un-gz '${output_unaligned_reads_l}'
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137 #else if $compressed == "BZ2":
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138 --un-bz2 '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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139 #else:
18
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140 --un '${output_unaligned_reads_l}'
14
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141 #end if
18
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142 #end if
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143 #if str( $library.aligned_file ) == "true":
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144 #if $compressed == "GZ":
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145 --al-gz '${output_aligned_reads_l}'
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146 #else if $compressed == "BZ2":
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147 --al-bz2 '${output_aligned_reads_l}'
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148 #else:
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149 --al '${output_aligned_reads_l}'
16
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150 #end if
18
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151 #end if
15
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152
18
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153 #elif str( $library.type ) == "paired_interleaved":
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154 --interleaved '${read1}'
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155 #if str( $library.unaligned_file ) == "true":
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156 #if $compressed == "GZ":
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157 --un-gz '${output_unaligned_reads_l}'
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158 #else if $compressed == "BZ2":
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159 --un-bz2 '${output_unaligned_reads_l}'
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160 #else:
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161 --un '${output_unaligned_reads_l}'
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162 #end if
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163 #end if
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164 #if str( $library.aligned_file ) == "true":
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165 #if $compressed == "GZ":
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diff changeset
166 --al-gz '${output_aligned_reads_l}'
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167 #else if $compressed == "BZ2":
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168 --al-bz2 '${output_aligned_reads_l}'
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169 #else:
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170 --al '${output_aligned_reads_l}'
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171 #end if
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172 #end if
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173 #else:
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174 -1 '${read1}'
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175 -2 '${read2}'
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176 #if str( $library.unaligned_file ) == "true":
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177 #if $compressed == "GZ":
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178 --un-conc-gz '${output_unaligned_reads_l}'
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179 #else if $compressed == "BZ2":
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180 --un-conc-bz2 '${output_unaligned_reads_l}'
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181 #else:
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182 --un-conc '${output_unaligned_reads_l}'
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183 #end if
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184 #end if
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185 #if str( $library.aligned_file ) == "true":
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186 #if $compressed == "GZ":
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187 --al-conc-gz '${output_aligned_reads_l}'
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188 #else if $compressed == "BZ2":
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189 --al-conc-bz2 '${output_aligned_reads_l}'
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190 #else:
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191 --al-conc '${output_aligned_reads_l}'
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192 #end if
18
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193 #end if
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194 #if str( $library.paired_options.paired_options_selector ) == "yes":
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195 -I ${library.paired_options.I}
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196 -X ${library.paired_options.X}
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197 ${library.paired_options.fr_rf_ff}
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198 ${library.paired_options.no_mixed}
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199 ${library.paired_options.no_discordant}
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200 ${library.paired_options.dovetail}
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201 ${library.paired_options.no_contain}
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202 ${library.paired_options.no_overlap}
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203 #end if
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204 #end if
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205
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206 ## Read group information.
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207 @define_read_group_helpers@
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208 #if str( $library.type ) == "single":
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209 #set $rg_auto_name = $read_group_name_default($library.input_1)
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210 #elif str( $library.type ) == "paired":
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211 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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212 #else
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213 #set $rg_auto_name = $read_group_name_default($library.input_1)
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214 #end if
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215 @set_use_rg_var@
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216 @set_read_group_vars@
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217 #if $use_rg
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218 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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219 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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220 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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221 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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222 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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223 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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224 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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225 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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226 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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227 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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228 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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229 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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230 #end if
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231
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232 ## Analysis type
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233 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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234 $analysis_type.presets
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235 #elif str( $analysis_type.analysis_type_selector ) == "full":
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236 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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237 --skip ${analysis_type.input_options.skip}
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238 --qupto ${analysis_type.input_options.qupto}
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239 --trim5 ${analysis_type.input_options.trim5}
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240 --trim3 ${analysis_type.input_options.trim3}
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241 ${analysis_type.input_options.qv_encoding}
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242 ${analysis_type.input_options.solexa_quals}
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243 ${analysis_type.input_options.int_quals}
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244 #end if
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245
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246 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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247 -N ${analysis_type.alignment_options.N}
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248 -L ${analysis_type.alignment_options.L}
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249 -i '${analysis_type.alignment_options.i}'
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250 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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251 --dpad ${analysis_type.alignment_options.dpad}
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252 --gbar ${analysis_type.alignment_options.gbar}
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253 ${analysis_type.alignment_options.ignore_quals}
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254 ${analysis_type.alignment_options.nofw}
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255 ${analysis_type.alignment_options.norc}
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256 ${analysis_type.alignment_options.no_1mm_upfront}
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257 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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258 --end-to-end
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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260 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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261 --local
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262 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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263 #end if
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264 #end if
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265
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266 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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267 #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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268 --ma ${analysis_type.scoring_options.ma}
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269 #end if
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270 --mp '${analysis_type.scoring_options.mp}'
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271 --np ${analysis_type.scoring_options.np}
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272 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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273 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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274 #end if
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275
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276 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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277 -k ${analysis_type.reporting_options.k}
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278 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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279 -a
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280 #end if
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281
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282 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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283 -D ${analysis_type.effort_options.D}
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284 -R ${analysis_type.effort_options.R}
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285 #end if
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286 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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287 ${analysis_type.other_options.non_deterministic}
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288 --seed ${analysis_type.other_options.seed}
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289 #end if
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290
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291 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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292 ${analysis_type.cline}
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293 #end if
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294
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295 #if str( $sam_options.sam_options_selector ) == "yes":
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296 ${sam_options.no_unal}
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297 ${sam_options.omit_sec_seq}
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298 ${sam_options.sam_no_qname_trunc}
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299 ${sam_options.xeq}
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300 ${sam_options.soft_clipped_unmapped_tlen}
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301 ${sam_options.reorder}
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302 #end if
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303
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304 ## mapping stats (i.e. stderr from bowtie2)
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305 #if $save_mapping_stats
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306 2> '$mapping_stats'
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307 #end if
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308
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309 ## output file
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310 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
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311 | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
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312 #else if $sam_options.reorder:
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313 | samtools view --no-PG -bS - -o '$output'
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314 #else:
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315 > '$output'
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316 #end if
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317
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318 ## rename unaligned sequence files
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319 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
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320 #from os.path import splitext
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321 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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322 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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323 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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324 #end if
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325 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
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326 #from os.path import splitext
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327 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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328 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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329 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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330 #end if
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331
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332 ]]></command>
0
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333 <inputs>
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334 <!-- single/paired -->
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335 <conditional name="library">
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336 <param name="type" type="select" label="Is this single or paired library">
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337 <option value="single">Single-end</option>
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338 <option value="paired">Paired-end</option>
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339 <option value="paired_collection">Paired-end Dataset Collection</option>
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340 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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341 </param>
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342
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343 <when value="single">
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344 <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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345 <expand macro="align_unalign" />
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346 </when>
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347 <when value="paired">
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348 <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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349 <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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350 <expand macro="align_unalign" />
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351 <expand macro="paired_end_options" />
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352 </when>
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353 <when value="paired_collection">
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354 <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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355 <expand macro="align_unalign" />
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356 <expand macro="paired_end_options" />
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357 </when>
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358 <when value="paired_interleaved">
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359 <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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360 <expand macro="align_unalign" />
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361 <expand macro="paired_end_options" />
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362 </when>
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363 </conditional>
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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 <!-- read group settings -->
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383 <expand macro="read_group_conditional" />
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384 <conditional name="analysis_type">
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385 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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386 <option value="simple">1: Default setting only</option>
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387 <option value="full">2: Full parameter list</option>
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388 </param>
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389 <when value="simple">
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390 <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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391 <option value="no_presets" selected="True">No, just use defaults</option>
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392 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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393 <option value="--fast">Fast end-to-end (--fast)</option>
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394 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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395 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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396 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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397 <option value="--fast-local">Fast local (--fast-local)</option>
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398 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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399 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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400 </param>
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401 </when>
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402 <when value="full">
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403 <conditional name="input_options">
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404 <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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405 <option value="yes">Yes</option>
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406 <option value="no" selected="true">No</option>
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407 </param>
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408 <when value="yes">
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409 <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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410 <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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411 <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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412 <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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413 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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414 <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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415 <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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416 </param>
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417 <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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418 <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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419 </when>
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420 <when value="no">
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421 <!-- do nothing -->
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422 </when>
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423 </conditional>
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424 <conditional name="alignment_options">
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425 <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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426 <option value="yes">Yes</option>
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427 <option value="no" selected="true">No</option>
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428 </param>
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429 <when value="yes">
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430 <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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431 <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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432 <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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433 <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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434 <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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435 <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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436 <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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437 <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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438 <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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439 <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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440 <conditional name="align_mode">
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441 <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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442 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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443 <option value="local">Local (--local)</option>
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444 </param>
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445 <when value="end-to-end">
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446 <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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447 </when>
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448 <when value="local">
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449 <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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450 </when>
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451 </conditional>
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452 </when>
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453 <when value="no">
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454 <!-- do nothing -->
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455 </when>
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456 </conditional>
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457 <conditional name="scoring_options">
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458 <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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459 <option value="yes">Yes</option>
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460 <option value="no" selected="true">No</option>
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461 </param>
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462 <when value="yes">
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463 <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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464 <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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465 <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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466 <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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467 <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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468 <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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469 <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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470 </when>
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471 <when value="no">
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472 <!-- do nothing -->
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473 </when>
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474 </conditional>
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475 <conditional name="reporting_options">
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476 <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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477 <option value="no" selected="true">No, do not set</option>
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478 <option value="k">Set -k option and enter -k value</option>
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479 <option value="a">Set -a option</option>
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480 </param>
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481 <when value="no">
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482 <!-- do nothing -->
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483 </when>
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484 <when value="k">
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485 <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"/>
2
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486 </when>
5
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487 <when value="a">
2
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488 <!-- do nothing here; set -a flag on the command line-->
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489 </when>
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490 </conditional>
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491 <conditional name="effort_options">
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492 <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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493 <option value="yes">Yes</option>
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494 <option value="no" selected="true">No</option>
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495 </param>
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496 <when value="yes">
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497 <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"/>
2
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498 <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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499 </when>
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500 <when value="no">
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501 <!-- do nothing -->
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502 </when>
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503 </conditional>
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504 <conditional name="other_options">
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505 <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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506 <option value="yes">Yes</option>
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507 <option value="no" selected="true">No</option>
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508 </param>
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509 <when value="yes">
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510 <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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511 <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"/>
2
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512 </when>
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513 <when value="no">
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514 <!-- do nothing -->
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515 </when>
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516 </conditional>
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517 </when>
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518 </conditional>
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519 <conditional name="sam_options">
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520 <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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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="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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526 <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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527 <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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528 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
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529 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
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530 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
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531 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
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532 label="Reorder output to reflect order of the input file"
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533 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
0
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534 </when>
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535 <when value="no"/>
0
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536 </conditional>
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537 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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538 </inputs>
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539 <!-- define outputs -->
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540 <outputs>
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541 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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542 <filter>library['unaligned_file'] is True</filter>
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543 <actions>
5
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544 <conditional name="library.type">
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545 <when value="single">
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546 <action type="format">
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547 <option type="from_param" name="library.input_1" param_attribute="ext" />
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548 </action>
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549 </when>
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550 <when value="paired">
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551 <action type="format">
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552 <option type="from_param" name="library.input_1" param_attribute="ext" />
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553 </action>
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554 </when>
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555 <when value="paired_collection">
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556 <action type="format">
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557 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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558 </action>
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559 </when>
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560 </conditional>
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561 <expand macro="dbKeyActions" />
0
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562 </actions>
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563 </data>
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564 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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565 <filter>library['aligned_file'] is True</filter>
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566 <actions>
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567 <conditional name="library.type">
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568 <when value="single">
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569 <action type="format">
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570 <option type="from_param" name="library.input_1" param_attribute="ext" />
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571 </action>
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572 </when>
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573 <when value="paired">
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574 <action type="format">
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575 <option type="from_param" name="library.input_1" param_attribute="ext" />
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576 </action>
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577 </when>
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578 <when value="paired_collection">
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579 <action type="format">
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580 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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581 </action>
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582 </when>
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583 </conditional>
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parents: 22
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584 <expand macro="dbKeyActions" />
11
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585 </actions>
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586 </data>
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diff changeset
587 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
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diff changeset
588 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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parents: 10
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589 <actions>
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parents: 10
diff changeset
590 <conditional name="library.type">
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parents: 10
diff changeset
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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parents: 10
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595 </when>
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596 <when value="paired_collection">
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parents: 10
diff changeset
597 <action type="format">
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parents: 10
diff changeset
598 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 10
diff changeset
599 </action>
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parents: 10
diff changeset
600 </when>
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601 </conditional>
23
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iuc
parents: 22
diff changeset
602 <expand macro="dbKeyActions" />
11
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parents: 10
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603 </actions>
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parents: 10
diff changeset
604 </data>
0
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605 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
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parents: 1
diff changeset
606 <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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parents:
diff changeset
607 <actions>
5
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parents: 2
diff changeset
608 <conditional name="library.type">
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diff changeset
609 <when value="paired">
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parents: 2
diff changeset
610 <action type="format">
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parents: 2
diff changeset
611 <option type="from_param" name="library.input_2" param_attribute="ext" />
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parents: 2
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612 </action>
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613 </when>
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parents: 2
diff changeset
614 <when value="paired_collection">
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parents: 2
diff changeset
615 <action type="format">
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diff changeset
616 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 2
diff changeset
617 </action>
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618 </when>
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diff changeset
619 </conditional>
23
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diff changeset
620 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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621 </actions>
a03a7ee6cdff Imported from capsule None
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622 </data>
24
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iuc
parents: 23
diff changeset
623 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
22
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parents: 21
diff changeset
624 <change_format>
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parents: 21
diff changeset
625 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
24
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parents: 23
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626 <when input="sam_options.sam_opt" value="true" format="sam" />
22
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parents: 21
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627 </change_format>
0
a03a7ee6cdff Imported from capsule None
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628 <actions>
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629 <conditional name="reference_genome.source">
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630 <when value="indexed">
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631 <action type="metadata" name="dbkey">
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parents:
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632 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
a03a7ee6cdff Imported from capsule None
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parents:
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633 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
a03a7ee6cdff Imported from capsule None
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parents:
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634 <filter type="param_value" ref="reference_genome.index" column="0"/>
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635 </option>
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636 </action>
a03a7ee6cdff Imported from capsule None
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637 </when>
a03a7ee6cdff Imported from capsule None
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638 <when value="history">
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parents:
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639 <action type="metadata" name="dbkey">
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640 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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641 </action>
a03a7ee6cdff Imported from capsule None
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642 </when>
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643 </conditional>
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parents: 22
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644 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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645 </actions>
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646 </data>
10
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parents: 8
diff changeset
647 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
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diff changeset
648 <filter>save_mapping_stats is True</filter>
23
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iuc
parents: 22
diff changeset
649 <actions>
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iuc
parents: 22
diff changeset
650 <expand macro="dbKeyActions" />
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parents: 22
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651 </actions>
10
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diff changeset
652 </data>
0
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653 </outputs>
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parents:
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654 <tests>
24
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655 <test expect_num_outputs="1">
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parents: 16
diff changeset
656 <!-- test on paired-end datasets -->
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parents: 1
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657 <param name="type" value="paired"/>
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parents: 1
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658 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
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659 <param name="unaligned_file" value="false"/>
2
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parents: 1
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660 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
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661 <param name="source" value="history" />
2
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parents: 1
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662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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parents: 1
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664 <param name="own_file" value="bowtie2-ref.fasta" />
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665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
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666 </test>
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parents: 24
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667 <test expect_num_outputs="3">
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parents: 24
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668 <!-- test on list paired collection -->
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parents: 16
diff changeset
669 <param name="type" value="paired_collection"/>
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parents: 16
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670 <param name="paired_options_selector" value="no"/>
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parents: 24
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671 <param name="unaligned_file" value="true"/>
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parents: 16
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672 <param name="analysis_type_selector" value="simple"/>
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iuc
parents: 16
diff changeset
673 <param name="source" value="history" />
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iuc
parents: 16
diff changeset
674 <param name="input_1">
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parents: 16
diff changeset
675 <collection type="paired">
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iuc
parents: 16
diff changeset
676 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
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parents: 16
diff changeset
677 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
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parents: 16
diff changeset
678 </collection>
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parents: 16
diff changeset
679 </param>
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parents: 16
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680 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 29
diff changeset
681 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
17
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parents: 16
diff changeset
682 </test>
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parents: 23
diff changeset
683 <test expect_num_outputs="1">
17
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parents: 16
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684 <!-- test on paired-end datasets with read group info -->
5
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parents: 2
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685 <param name="type" value="paired"/>
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parents: 2
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686 <param name="paired_options_selector" value="no"/>
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parents: 2
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687 <param name="unaligned_file" value="false"/>
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parents: 2
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688 <param name="analysis_type_selector" value="simple"/>
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689 <param name="rg_selector" value="set"/>
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690 <param name="ID" value="rg1"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
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691 <param name="PL" value="CAPILLARY"/>
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692 <param name="source" value="history" />
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parents: 2
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693 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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parents: 2
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694 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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695 <param name="own_file" value="bowtie2-ref.fasta" />
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696 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/>
5
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697 </test>
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iuc
parents: 23
diff changeset
698 <test expect_num_outputs="2">
17
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parents: 16
diff changeset
699 <!-- test on paired-end datasets with stats output -->
10
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parents: 8
diff changeset
700 <param name="type" value="paired"/>
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devteam
parents: 8
diff changeset
701 <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
702 <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
703 <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
704 <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
705 <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
706 <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
707 <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
708 <param name="save_mapping_stats" value="true" />
30
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iuc
parents: 29
diff changeset
709 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
15
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iuc
parents: 14
diff changeset
710 <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
711 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
712 <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
713 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
714 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
715 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
716 <test expect_num_outputs="1">
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
717 <!-- 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
718 <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
719 <!-- <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
720 <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
721 <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
722 <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
723 <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
724 <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
725 <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
726 <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
727 <param name="own_file" value="bowtie2-ref.fasta" />
30
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iuc
parents: 29
diff changeset
728 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
729 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
730 <test expect_num_outputs="1">
17
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iuc
parents: 16
diff changeset
731 <!-- test on fastqsanger.gz paired-end datasets -->
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
732 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
733 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
734 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
735 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
736 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
737 <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
738 <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
devteam
parents: 13
diff changeset
739 <param name="own_file" value="bowtie2-ref.fasta" />
30
2f3400246bfc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
iuc
parents: 29
diff changeset
740 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
741 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
742 <test expect_num_outputs="1">
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
743 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
746 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
747 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
748 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
749 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
750 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
751 <param name="own_file" value="bowtie2-ref.fasta" />
30
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iuc
parents: 29
diff changeset
752 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
754 <test expect_num_outputs="1">
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
755 <!-- test on fasta paired-end datasets -->
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
756 <param name="type" value="paired"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
757 <param name="paired_options_selector" value="no"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
758 <param name="unaligned_file" value="false"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
759 <param name="analysis_type_selector" value="simple"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
760 <param name="source" value="history" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
761 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
762 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
763 <param name="own_file" value="bowtie2-ref.fasta" />
30
2f3400246bfc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
iuc
parents: 29
diff changeset
764 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/>
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
765 </test>
24
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iuc
parents: 23
diff changeset
766 <test expect_num_outputs="1">
22
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iuc
parents: 21
diff changeset
767 <!-- test on fasta paired-end datasets with bam_native as output -->
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
768 <param name="type" value="paired"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
769 <param name="paired_options_selector" value="no"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
770 <param name="unaligned_file" value="false"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
771 <param name="analysis_type_selector" value="simple"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
772 <param name="source" value="history" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
773 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
774 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
775 <param name="own_file" value="bowtie2-ref.fasta" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
776 <param name="sam_options_selector" value="yes" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
777 <param name="reorder" value="true" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
778 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
779 </test>
24
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iuc
parents: 23
diff changeset
780 <test expect_num_outputs="1">
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781 <!-- test on fasta paired-end datasets with sam as output -->
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782 <param name="type" value="paired"/>
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783 <param name="paired_options_selector" value="no"/>
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784 <param name="unaligned_file" value="false"/>
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785 <param name="analysis_type_selector" value="simple"/>
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786 <param name="source" value="history" />
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787 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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788 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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789 <param name="own_file" value="bowtie2-ref.fasta" />
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790 <param name="sam_options_selector" value="yes" />
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791 <param name="sam_options|sam_opt" value="true" />
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792 <output name="output" ftype="sam">
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793 <assert_contents>
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794 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
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795 </assert_contents>
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796 </output>
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797 </test>
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798 </tests>
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799 <help><![CDATA[
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800 **Bowtie2 Overview**
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801
2
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802 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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803 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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804
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805 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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806 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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807 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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808
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809 -----
0
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810
2
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811 **Selecting reference genomes for Bowtie2**
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812
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813 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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814
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815 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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816 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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817
2
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818 If your genome of interest is not listed here you have two choices:
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819
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820 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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821 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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822
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823 ------
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824
2
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825 .. class:: infomark
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826
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827 **Bowtie2 options**
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828
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829 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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830
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831 -----
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832
0
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833 **Inputs**
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834
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835 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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836
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837 ------
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838
2
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839 **Input options**::
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840
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841 --interleaved
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842 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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843
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844 -s/--skip <int>
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845 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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846
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847 -u/--qupto <int>
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848 Align the first `<int>` reads or read pairs from the input (after the
2
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849 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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850
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851 -5/--trim5 <int>
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852 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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853
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854 -3/--trim3 <int>
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855 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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856
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857 --phred33
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858 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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859 also called the "Phred+33" encoding, which is used by the very latest Illumina
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860 pipelines.
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861
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862 --phred64
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863 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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864 also called the "Phred+64" encoding.
0
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865
2
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866 --solexa-quals
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867 Convert input qualities from Solexa Phred quality (which can be negative) to
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868 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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869 Pipeline versions (prior to 1.3). Default: off.
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870
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871 --int-quals
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872 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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873 Integers are treated as being on the Phred quality scale unless
2
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874 `--solexa-quals` is also specified. Default: off.
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875
2
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876 ------
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877
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878 **Presets in `--end-to-end` mode**::
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879
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880 --very-fast
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881 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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882
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883 --fast
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884 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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885
2
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886 --sensitive
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887 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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888
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889 --very-sensitive
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890 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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891
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892 ------
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893
2
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894 **Presets options in `--local` mode**::
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895
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896 --very-fast-local
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897 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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898
2
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899 --fast-local
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900 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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901
2
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902 --sensitive-local
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903 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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904
2
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905 --very-sensitive-local
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906 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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907
0
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908 ------
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909
2
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910 **Alignment options**::
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911
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diff changeset
912 -N <int>
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913 Sets the number of mismatches to allowed in a seed alignment during multiseed
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diff changeset
914 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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915 (often much slower) but increases sensitivity. Default: 0.
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916
11
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diff changeset
917 -L <int>
5
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diff changeset
918 Sets the length of the seed substrings to align during multiseed alignment.
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diff changeset
919 Smaller values make alignment slower but more sensitive. Default: the
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diff changeset
920 `--sensitive` preset is used by default, which sets `-L` to 22 in
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diff changeset
921 `--end-to-end` mode and to 20 in `--local` mode.
2
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diff changeset
922
11
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diff changeset
923 -i <func>
2
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diff changeset
924 Sets a function governing the interval between seed substrings to use during
5
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diff changeset
925 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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926 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
927
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928 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
929 Seed 1 fw: TAGCTACGCT
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930 Seed 1 rc: AGCGTAGCTA
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diff changeset
931 Seed 2 fw: CGCTCTACGC
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932 Seed 2 rc: GCGTAGAGCG
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diff changeset
933 Seed 3 fw: ACGCTATCAT
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934 Seed 3 rc: ATGATAGCGT
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diff changeset
935 Seed 4 fw: TCATGCATAA
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diff changeset
936 Seed 4 rc: TTATGCATGA
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937
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diff changeset
938 Since it's best to use longer intervals for longer reads, this parameter sets
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diff changeset
939 the interval as a function of the read length, rather than a single
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940 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
2a6cfe8997aa Uploaded from GH
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diff changeset
941 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
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diff changeset
942 If the function returns a result less than
2
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943 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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944 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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945 in `--local` mode.
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946
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diff changeset
947 --n-ceil <func>
2
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948 Sets a function governing the maximum number of ambiguous characters (usually
2a6cfe8997aa Uploaded from GH
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diff changeset
949 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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diff changeset
950 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
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951 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
952 Default: `L,0,0.15`.
2
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953
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diff changeset
954 --dpad <int>
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diff changeset
955 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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956 gaps. Default: 15.
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957
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diff changeset
958 --gbar <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
959 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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960 Default: 4.
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961
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962 --ignore-quals
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963 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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964 mismatched position to be the highest possible, regardless of the actual value.
2
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965 I.e. input is treated as though all quality values are high. This is also the
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966 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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967 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
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968
2
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969 --nofw/--norc
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970 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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971 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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972 not attempt to align unpaired reads against the reverse-complement (Crick)
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973 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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974 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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975 paired-end configurations corresponding to fragments from the reverse-complement
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diff changeset
976 (Crick) strand. Default: both strands enabled.
2
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977
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978 --no-1mm-upfront
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979 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
5
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980 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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981 alignments can be found very quickly, and many short read alignments have exact or
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982 near-exact end-to-end alignments. However, this can lead to unexpected
5
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diff changeset
983 alignments when the user also sets options governing the multiseed heuristic,
2
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984 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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985 to the length of the read, the user will be surprised to find 1-mismatch alignments
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986 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
5
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diff changeset
987 alignments before using the multiseed heuristic, which leads to the expected
2
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988 behavior when combined with options such as `-L` and `-N`. This comes at the
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989 expense of speed.
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990
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991 --end-to-end
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992 In this mode, Bowtie 2 requires that the entire read align from one end to the
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993 other, without any trimming (or "soft clipping") of characters from either end.
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994 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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995 are less than or equal to 0, and the greatest possible alignment score is 0.
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996 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
a03a7ee6cdff Imported from capsule None
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997
2
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998 --local
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999 In this mode, Bowtie 2 does not require that the entire read align from one end
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1000 to the other. Rather, some characters may be omitted ("soft clipped") from the
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1001 ends in order to achieve the greatest possible alignment score. The match bonus
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1002 `--ma` is used in this mode, and the best possible alignment score is equal to
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1003 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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1004 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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1005 the local version of the preset (`--very-fast-local`). This is mutually
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1006 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1007
2
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1008 -----
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1009
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1010 **Scoring options**::
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1011
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diff changeset
1012 --ma <int>
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diff changeset
1013 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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1014 score for each position where a read character aligns to a reference character
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1015 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1016
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1017 --mp MX,MN
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1018 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1019 number less than or equal to `MX` and greater than or equal to `MN` is
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1020 subtracted from the alignment score for each position where a read character
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1021 aligns to a reference character, the characters do not match, and neither is an
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1022 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1023 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1024 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1025
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1026 --np <int>
2
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1027 Sets penalty for positions where the read, reference, or both, contain an
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1028 ambiguous character such as `N`. Default: 1.
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1029
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1030 --rdg <int1>,<int2>
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1031 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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1032 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1033
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1034 --rfg <int1>,<int2>
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1035 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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1036 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1037 5, 3.
0
a03a7ee6cdff Imported from capsule None
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1038
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1039 --score-min <func>
2
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1040 Sets a function governing the minimum alignment score needed for an alignment to
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1041 be considered "valid" (i.e. good enough to report). This is a function of read
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1042 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
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1043 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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1044 the default in `--local` mode is `G,20,8`.
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1045
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1046 -----
2
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1047
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1048 **Reporting options**::
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1049
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1050 -k <int>
2
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1051 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1052 When it finds a valid alignment, it continues looking for alignments that are
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1053 nearly as good or better. The best alignment found is reported (randomly
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1054 selected from among best if tied). Information about the best alignments is
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1055 used to estimate mapping quality and to set SAM optional fields, such as
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1056 `AS:i` and `XS:i`.
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1057
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1058 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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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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diff changeset
1059 searches for at most `<int>` distinct, valid alignments for each read. The
2
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diff changeset
1060 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
1061 finds `<int>`, whichever happens first. All alignments found are reported in
2
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diff changeset
1062 descending order by alignment score. The alignment score for a paired-end
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diff changeset
1063 alignment equals the sum of the alignment scores of the individual mates. Each
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diff changeset
1064 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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parents: 1
diff changeset
1065 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1066 `<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
1067 `<int>` alignments reported are the best possible in terms of alignment score.
2
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diff changeset
1068 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1069
2
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diff changeset
1070 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
2a6cfe8997aa Uploaded from GH
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diff changeset
1071 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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diff changeset
1072
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diff changeset
1073 -a
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diff changeset
1074 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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diff changeset
1075 is mutually exclusive with `-k`.
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diff changeset
1076
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diff changeset
1077 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
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diff changeset
1078 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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diff changeset
1079
2
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diff changeset
1080 -----
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diff changeset
1081
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diff changeset
1082 **Effort options**::
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1083
11
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diff changeset
1084 -D <int>
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diff changeset
1085 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1086 moves on, using the alignments found so far. A seed extension "fails" if it
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diff changeset
1087 does not yield a new best or a new second-best alignment. This limit is
2a6cfe8997aa Uploaded from GH
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1088 automatically adjusted up when -k or -a are specified. Default: 15.
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diff changeset
1089
11
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diff changeset
1090 -R <int>
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diff changeset
1091 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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diff changeset
1092 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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diff changeset
1093 (same length, same number of mismatches allowed) at different offsets and
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diff changeset
1094 searches for more alignments. A read is considered to have repetitive seeds if
2a6cfe8997aa Uploaded from GH
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diff changeset
1095 the total number of seed hits divided by the number of seeds that aligned at
2a6cfe8997aa Uploaded from GH
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diff changeset
1096 least once is greater than 300. Default: 2.
11
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diff changeset
1097
2
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diff changeset
1098 -----
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diff changeset
1099
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diff changeset
1100 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
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1101
11
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diff changeset
1102 -I/--minins <int>
2
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1103 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
2a6cfe8997aa Uploaded from GH
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1104 specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
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diff changeset
1105 appropriate orientation with a 20-bp gap between them, that alignment is
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diff changeset
1106 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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diff changeset
1107 be valid in that case. If trimming options `-3` or `-5` are also used, the
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diff changeset
1108 `-I` constraint is applied with respect to the untrimmed mates.
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diff changeset
1109
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diff changeset
1110 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
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diff changeset
1111 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
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diff changeset
1112 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1113 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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diff changeset
1114 efficient.
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1115
11
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diff changeset
1116 Default: 0 (essentially imposing no minimum)
2
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1117
11
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diff changeset
1118 -X/--maxins <int>
2
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diff changeset
1119 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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diff changeset
1120 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1121 proper orientation with a 60-bp gap between them, that alignment is considered
2a6cfe8997aa Uploaded from GH
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diff changeset
1122 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
2a6cfe8997aa Uploaded from GH
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diff changeset
1123 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1124 constraint is applied with respect to the untrimmed mates, not the trimmed
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diff changeset
1125 mates.
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diff changeset
1126
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1127 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1128 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1129 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1130 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1131 efficient.
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1132
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1133 Default: 500.
0
a03a7ee6cdff Imported from capsule None
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1134
2
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1135 --fr/--rf/--ff
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1136 The upstream/downstream mate orientations for a valid paired-end alignment
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1137 against the forward reference strand. E.g., if `--fr` is specified and there is
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diff changeset
1138 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1139 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1140 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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diff changeset
1141 complement of mate 1 and all other constraints are met, that too is valid.
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1142 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1143 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1144 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1145 for Illumina's Paired-end Sequencing Assay).
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diff changeset
1146
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1147 --no-mixed
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1148 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1149 a pair, it then tries to find alignments for the individual mates. This option
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diff changeset
1150 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1151
2
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1152 --no-discordant
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1153 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1154 concordant alignments. A discordant alignment is an alignment where both mates
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1155 align uniquely, but that does not satisfy the paired-end constraints
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1156 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1157
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1158 --dovetail
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1159 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
1160 beginning of the other such that the wrong mate begins upstream, consider that
5
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diff changeset
1161 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1162
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1163 --no-contain
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1164 If one mate alignment contains the other, consider that to be non-concordant.
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1165 Default: a mate can contain the other in a concordant alignment.
2
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1166
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1167 --no-overlap
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1168 If one mate alignment overlaps the other at all, consider that to be
5
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diff changeset
1169 non-concordant. Default: mates can overlap in a concordant alignment.
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1170
0
a03a7ee6cdff Imported from capsule None
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1171 ------
a03a7ee6cdff Imported from capsule None
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1172
2
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diff changeset
1173 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
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1174
11
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diff changeset
1175 --rg-id <text>
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1176 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1177 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1178 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1179 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1180
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diff changeset
1181 --rg <text>
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1182 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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1183 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
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diff changeset
1184 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1185 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1186 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1187
2
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1188 --omit-sec-seq
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diff changeset
1189 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1190 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1191 in those fields instead.
11
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diff changeset
1192
2
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1193 -----
0
a03a7ee6cdff Imported from capsule None
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1194
2
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1195 **Other options**::
0
a03a7ee6cdff Imported from capsule None
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1196
2
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1197 --reorder
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1198 Guarantees that output SAM records are printed in an order corresponding to the
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1199 order of the reads in the original input file, even when `-p` is set greater
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1200 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1201 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1202 not specified. Has no effect if `-p` is set to 1, since output order will
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1203 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
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1204
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diff changeset
1205 --seed <int>
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diff changeset
1206 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
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1207
2
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diff changeset
1208 --non-deterministic
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1209 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1210 seeds the generator with a number derived from (a) the read name, (b) the
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1211 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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parents: 1
diff changeset
1212 option. This means that if two reads are identical (same name, same
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1213 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1214 for both, even if there was ambiguity. When `--non-deterministic` is specified,
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1215 Bowtie 2 re-initializes its pseudo-random generator for each read using the
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1216 current time. This means that Bowtie 2 will not necessarily report the same
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1217 alignment for two identical reads. This is counter-intuitive for some users,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1218 but might be more appropriate in situations where the input consists of many
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1219 identical reads.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1220
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1221 -----
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
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1224 **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
iuc
parents: 14
diff changeset
1225
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1226 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
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 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
1229
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
1230 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1231 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1232 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1233 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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 @2/1
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iuc
parents: 14
diff changeset
1235 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
1236 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1237 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
1238
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parents: 14
diff changeset
1239 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
1240
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
1241 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1242 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
1243 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1244 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1245 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1246 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1247 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1248 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
1249
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parents: 14
diff changeset
1250 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
1251
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
1252 @1/1
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parents: 14
diff changeset
1253 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
1254 +
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parents: 14
diff changeset
1255 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
1256 @1/2
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parents: 14
diff changeset
1257 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
1258 +
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
1259 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
1260 @2/1
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parents: 14
diff changeset
1261 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
1262 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1263 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1264 @2/2
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parents: 14
diff changeset
1265 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
1266 +
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parents: 14
diff changeset
1267 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
1268 ]]></help>
2
2a6cfe8997aa Uploaded from GH
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1269 <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
1270 <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
iuc
parents: 16
diff changeset
1271 <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
1272 </citations>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1273 </tool>