Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 28:8681e741a037 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
author iuc
date Sat, 10 Jul 2021 07:44:43 +0000
parents c9105910063f
children 56dcf3929d02
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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
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2 <description>- map reads against reference genome</description>
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
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5 </macros>
11
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6 <requirements>
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c9105910063f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
c9105910063f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
iuc
parents: 26
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8 <requirement type="package" version="1.11">samtools</requirement>
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9 </requirements>
0
a03a7ee6cdff Imported from capsule None
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10 <version_command>bowtie2 --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
21
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12 ## 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
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13 set -o | grep -q pipefail && set -o pipefail;
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iuc
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14 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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15 #set index_path = ''
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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16 #if str($reference_genome.source) == "history":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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18 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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19 #set index_path = 'genome'
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20 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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21 #set index_path = $reference_genome.index.fields.path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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22 #end if
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23
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24 ## Link in the input files, so bowtie2 can tell their type
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26 #set compressed="False"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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27 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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28 #if str($library.type) == 'paired':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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29 #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
iuc
parents: 17
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30 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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31 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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parents: 17
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32 #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
iuc
parents: 17
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33 #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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34 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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35 #else if $library.input_1.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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37 #set read1 = "input_f.fasta"
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38 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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39 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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40 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 ln -f -s '${library.input_1}' ${read1} &&
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42
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43 #if $library.input_2.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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44 #set read2 = "input_r.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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45 #set compressed = "GZ"
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46 #else if $library.input_2.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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47 #set read2 = "input_r.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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48 #set compressed = "BZ2"
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49 #else if $library.input_2.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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50 #set read2 = "input_r.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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51 #else:
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52 #set read2 = "input_r.fastq"
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53 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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54 ln -f -s '${library.input_2}' ${read2} &&
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55 #else if str($library.type) == 'paired_collection':
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56 #if $library.input_1.forward.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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57 #set read1 = "input_f.fastq.gz"
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58 #set compressed = "GZ"
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59 #else if $library.input_1.forward.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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60 #set read1 = "input_f.fastq.bz2"
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61 #set compressed = "BZ2"
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62 #else if $library.input_1.forward.is_of_type('fasta'):
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63 #set reads_are_fastq = False
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64 #set read1 = "input_f.fasta"
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65 #else:
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66 #set read1 = "input_f.fastq"
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67 #end if
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68 ln -s '${library.input_1.forward}' ${read1} &&
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69
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70 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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71 #set read2 = "input_r.fastq.gz"
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72 #set compressed = "GZ"
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73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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74 #set read2 = "input_r.fastq.bz2"
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75 #set compressed = "BZ2"
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76 #else if $library.input_1.reverse.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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77 #set read2 = "input_r.fasta"
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78 #else:
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79 #set read2 = "input_r.fastq"
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80 #end if
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81 ln -s '${library.input_1.reverse}' ${read2} &&
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82
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83 #else if str($library.type) == 'paired_interleaved':
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84 #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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85 #set read1 = "input_il.fastq.gz"
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86 #set compressed = "GZ"
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87 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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88 #set read1 = "input_il.fastq.bz2"
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89 #set compressed = "BZ2"
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90 #else if $library.input_1.is_of_type("fasta"):
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91 #set reads_are_fastq = False
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92 #set read1 = "input_il.fasta"
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93 #else:
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94 #set read1 = "input_il.fastq"
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95 #end if
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96 ln -s '${library.input_1}' ${read1} &&
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97 #else:
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98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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99 #set read1 = "input_f.fastq.gz"
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100 #set compressed = "GZ"
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101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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102 #set read1 = "input_f.fastq.bz2"
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103 #set compressed = "BZ2"
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104 #else if $library.input_1.is_of_type("fasta"):
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105 #set reads_are_fastq = False
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106 #set read1 = "input_f.fasta"
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107 #else:
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108 #set read1 = "input_f.fastq"
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109 #end if
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110 ln -s '${library.input_1}' ${read1} &&
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111 #end if
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112
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113 ## execute bowtie2
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114
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115 bowtie2
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116
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117 ## number of threads
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118 -p \${GALAXY_SLOTS:-4}
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119
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120 ## index file path
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121 -x '$index_path'
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122
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123 ## Input reads are fasta?
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124 #if not reads_are_fastq:
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125 -f
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126 #end if
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127
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128 ## Input reads
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129 #if str( $library.type ) == "single":
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130 -U '${read1}'
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131 #if str( $library.unaligned_file ) == "true":
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132 #if $compressed == "GZ":
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133 --un-gz '${output_unaligned_reads_l}'
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134 #else if $compressed == "BZ2":
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135 --un-bz2 '${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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136 #else:
18
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137 --un '${output_unaligned_reads_l}'
14
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138 #end if
18
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139 #end if
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140 #if str( $library.aligned_file ) == "true":
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141 #if $compressed == "GZ":
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142 --al-gz '${output_aligned_reads_l}'
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143 #else if $compressed == "BZ2":
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144 --al-bz2 '${output_aligned_reads_l}'
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145 #else:
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146 --al '${output_aligned_reads_l}'
16
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147 #end if
18
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148 #end if
15
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149
18
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150 #elif str( $library.type ) == "paired_interleaved":
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151 --interleaved '${read1}'
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152 #if str( $library.unaligned_file ) == "true":
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153 #if $compressed == "GZ":
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154 --un-gz '${output_unaligned_reads_l}'
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155 #else if $compressed == "BZ2":
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156 --un-bz2 '${output_unaligned_reads_l}'
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157 #else:
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158 --un '${output_unaligned_reads_l}'
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159 #end if
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160 #end if
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161 #if str( $library.aligned_file ) == "true":
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162 #if $compressed == "GZ":
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163 --al-gz '${output_aligned_reads_l}'
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164 #else if $compressed == "BZ2":
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165 --al-bz2 '${output_aligned_reads_l}'
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166 #else:
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167 --al '${output_aligned_reads_l}'
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168 #end if
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169 #end if
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170 #else:
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171 -1 '${read1}'
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172 -2 '${read2}'
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173 #if str( $library.unaligned_file ) == "true":
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174 #if $compressed == "GZ":
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175 --un-conc-gz '${output_unaligned_reads_l}'
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176 #else if $compressed == "BZ2":
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177 --un-conc-bz2 '${output_unaligned_reads_l}'
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178 #else:
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179 --un-conc '${output_unaligned_reads_l}'
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180 #end if
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181 #end if
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182 #if str( $library.aligned_file ) == "true":
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183 #if $compressed == "GZ":
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184 --al-conc-gz '${output_aligned_reads_l}'
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185 #else if $compressed == "BZ2":
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186 --al-conc-bz2 '${output_aligned_reads_l}'
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187 #else:
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188 --al-conc '${output_aligned_reads_l}'
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189 #end if
18
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190 #end if
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191 #if str( $library.paired_options.paired_options_selector ) == "yes":
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192 -I ${library.paired_options.I}
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193 -X ${library.paired_options.X}
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194 ${library.paired_options.fr_rf_ff}
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195 ${library.paired_options.no_mixed}
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196 ${library.paired_options.no_discordant}
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197 ${library.paired_options.dovetail}
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198 ${library.paired_options.no_contain}
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199 ${library.paired_options.no_overlap}
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200 #end if
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201 #end if
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202
18
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203 ## Read group information.
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204 @define_read_group_helpers@
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205 #if str( $library.type ) == "single":
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206 #set $rg_auto_name = $read_group_name_default($library.input_1)
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207 #elif str( $library.type ) == "paired":
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208 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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209 #else
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210 #set $rg_auto_name = $read_group_name_default($library.input_1)
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211 #end if
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212 @set_use_rg_var@
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213 @set_read_group_vars@
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214 #if $use_rg
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215 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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216 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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217 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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218 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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219 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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220 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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221 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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222 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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223 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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224 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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225 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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226 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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227 #end if
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228
18
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229 ## Analysis type
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230 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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231 $analysis_type.presets
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232 #elif str( $analysis_type.analysis_type_selector ) == "full":
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233 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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234 --skip ${analysis_type.input_options.skip}
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235 --qupto ${analysis_type.input_options.qupto}
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236 --trim5 ${analysis_type.input_options.trim5}
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237 --trim3 ${analysis_type.input_options.trim3}
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238 ${analysis_type.input_options.qv_encoding}
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239 ${analysis_type.input_options.solexa_quals}
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240 ${analysis_type.input_options.int_quals}
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241 #end if
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242
18
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243 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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244 -N ${analysis_type.alignment_options.N}
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245 -L ${analysis_type.alignment_options.L}
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246 -i '${analysis_type.alignment_options.i}'
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247 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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248 --dpad ${analysis_type.alignment_options.dpad}
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249 --gbar ${analysis_type.alignment_options.gbar}
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250 ${analysis_type.alignment_options.ignore_quals}
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251 ${analysis_type.alignment_options.nofw}
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252 ${analysis_type.alignment_options.norc}
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253 ${analysis_type.alignment_options.no_1mm_upfront}
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254 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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255 --end-to-end
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256 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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257 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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258 --local
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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260 #end if
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261 #end if
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262
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263 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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264 #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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265 --ma ${analysis_type.scoring_options.ma}
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266 #end if
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267 --mp '${analysis_type.scoring_options.mp}'
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268 --np ${analysis_type.scoring_options.np}
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269 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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270 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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271 #end if
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272
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273 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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274 -k ${analysis_type.reporting_options.k}
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275 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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276 -a
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277 #end if
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278
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279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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280 -D ${analysis_type.effort_options.D}
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281 -R ${analysis_type.effort_options.R}
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282 #end if
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283 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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284 ${analysis_type.other_options.non_deterministic}
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285 --seed ${analysis_type.other_options.seed}
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286 #end if
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287
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288 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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289 ${analysis_type.cline}
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290 #end if
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291
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292 #if str( $sam_options.sam_options_selector ) == "yes":
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293 ${sam_options.no_unal}
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294 ${sam_options.omit_sec_seq}
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295 ${sam_options.sam_no_qname_trunc}
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296 ${sam_options.xeq}
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297 ${sam_options.soft_clipped_unmapped_tlen}
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298 ${sam_options.reorder}
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299 #end if
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300
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301 ## mapping stats (i.e. stderr from bowtie2)
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302 #if $save_mapping_stats
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303 2> '$mapping_stats'
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304 #end if
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305
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306 ## output file
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307 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
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308 | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
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309 #else if $sam_options.reorder:
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310 | samtools view --no-PG -bS - -o '$output'
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311 #else:
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312 > '$output'
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313 #end if
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314
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315 ## rename unaligned sequence files
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316 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
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317 #from os.path import splitext
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318 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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319 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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320 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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321 #end if
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322 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
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323 #from os.path import splitext
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324 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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325 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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326 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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327 #end if
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328
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329 ]]></command>
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330 <inputs>
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331 <!-- single/paired -->
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332 <conditional name="library">
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333 <param name="type" type="select" label="Is this single or paired library">
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334 <option value="single">Single-end</option>
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335 <option value="paired">Paired-end</option>
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336 <option value="paired_collection">Paired-end Dataset Collection</option>
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337 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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338 </param>
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339
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340 <when value="single">
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341 <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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342 <expand macro="align_unalign" />
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343 </when>
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344 <when value="paired">
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345 <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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346 <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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347 <expand macro="align_unalign" />
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348 <expand macro="paired_end_options" />
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349 </when>
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350 <when value="paired_collection">
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351 <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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352 <expand macro="align_unalign" />
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353 <expand macro="paired_end_options" />
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354 </when>
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355 <when value="paired_interleaved">
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356 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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357 <expand macro="align_unalign" />
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358 <expand macro="paired_end_options" />
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359 </when>
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360 </conditional>
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361 <!-- reference genome -->
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362 <conditional name="reference_genome">
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363 <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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364 <option value="indexed">Use a built-in genome index</option>
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365 <option value="history">Use a genome from the history and build index</option>
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366 </param>
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367 <when value="indexed">
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368 <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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369 <options from_data_table="bowtie2_indexes">
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370 <filter type="sort_by" column="2"/>
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371 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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372 </options>
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373 </param>
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374 </when>
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375 <when value="history">
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376 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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377 </when>
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378 </conditional>
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379 <!-- read group settings -->
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380 <expand macro="read_group_conditional" />
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381 <conditional name="analysis_type">
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382 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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383 <option value="simple">1: Default setting only</option>
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384 <option value="full">2: Full parameter list</option>
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385 </param>
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386 <when value="simple">
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387 <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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388 <option value="no_presets" selected="True">No, just use defaults</option>
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389 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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390 <option value="--fast">Fast end-to-end (--fast)</option>
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391 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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392 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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393 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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394 <option value="--fast-local">Fast local (--fast-local)</option>
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395 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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396 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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397 </param>
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398 </when>
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399 <when value="full">
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400 <conditional name="input_options">
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401 <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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402 <option value="yes">Yes</option>
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403 <option value="no" selected="true">No</option>
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404 </param>
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405 <when value="yes">
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406 <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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407 <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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408 <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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409 <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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410 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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411 <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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412 <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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413 </param>
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414 <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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415 <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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416 </when>
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417 <when value="no">
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418 <!-- do nothing -->
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419 </when>
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420 </conditional>
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421 <conditional name="alignment_options">
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422 <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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423 <option value="yes">Yes</option>
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424 <option value="no" selected="true">No</option>
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425 </param>
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426 <when value="yes">
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427 <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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428 <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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429 <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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430 <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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431 <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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432 <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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433 <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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434 <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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435 <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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436 <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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437 <conditional name="align_mode">
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438 <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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439 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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440 <option value="local">Local (--local)</option>
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441 </param>
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442 <when value="end-to-end">
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443 <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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444 </when>
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445 <when value="local">
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446 <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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447 </when>
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448 </conditional>
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449 </when>
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450 <when value="no">
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451 <!-- do nothing -->
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452 </when>
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453 </conditional>
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454 <conditional name="scoring_options">
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455 <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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456 <option value="yes">Yes</option>
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457 <option value="no" selected="true">No</option>
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458 </param>
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459 <when value="yes">
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460 <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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461 <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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462 <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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463 <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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464 <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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465 <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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466 <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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467 </when>
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468 <when value="no">
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469 <!-- do nothing -->
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470 </when>
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471 </conditional>
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472 <conditional name="reporting_options">
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473 <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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474 <option value="no" selected="true">No, do not set</option>
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475 <option value="k">Set -k option and enter -k value</option>
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476 <option value="a">Set -a option</option>
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477 </param>
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478 <when value="no">
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479 <!-- do nothing -->
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480 </when>
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481 <when value="k">
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482 <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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483 </when>
5
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484 <when value="a">
2
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485 <!-- do nothing here; set -a flag on the command line-->
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486 </when>
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487 </conditional>
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488 <conditional name="effort_options">
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489 <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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490 <option value="yes">Yes</option>
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491 <option value="no" selected="true">No</option>
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492 </param>
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493 <when value="yes">
5
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494 <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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495 <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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496 </when>
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497 <when value="no">
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498 <!-- do nothing -->
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499 </when>
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500 </conditional>
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501 <conditional name="other_options">
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502 <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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503 <option value="yes">Yes</option>
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504 <option value="no" selected="true">No</option>
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505 </param>
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506 <when value="yes">
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507 <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"/>
5
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508 <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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509 </when>
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510 <when value="no">
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511 <!-- do nothing -->
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512 </when>
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513 </conditional>
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514 </when>
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515 </conditional>
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516 <conditional name="sam_options">
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517 <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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518 <option value="yes">Yes</option>
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519 <option value="no" selected="true">No</option>
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520 </param>
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521 <when value="yes">
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522 <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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523 <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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524 <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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525 <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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526 <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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parents: 21
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527 <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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528 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
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529 label="Reorder output to reflect order of the input file"
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530 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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531 </when>
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532 <when value="no"/>
0
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533 </conditional>
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534 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
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535 </inputs>
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536 <!-- define outputs -->
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537 <outputs>
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538 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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539 <filter>library['unaligned_file'] is True</filter>
0
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540 <actions>
5
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541 <conditional name="library.type">
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542 <when value="single">
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543 <action type="format">
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544 <option type="from_param" name="library.input_1" param_attribute="ext" />
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545 </action>
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546 </when>
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547 <when value="paired">
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548 <action type="format">
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549 <option type="from_param" name="library.input_1" param_attribute="ext" />
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550 </action>
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551 </when>
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552 <when value="paired_collection">
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553 <action type="format">
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554 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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555 </action>
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556 </when>
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557 </conditional>
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558 <expand macro="dbKeyActions" />
0
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559 </actions>
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560 </data>
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561 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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562 <filter>library['aligned_file'] is True</filter>
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563 <actions>
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564 <conditional name="library.type">
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565 <when value="single">
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566 <action type="format">
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567 <option type="from_param" name="library.input_1" param_attribute="ext" />
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568 </action>
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569 </when>
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570 <when value="paired">
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571 <action type="format">
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572 <option type="from_param" name="library.input_1" param_attribute="ext" />
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573 </action>
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574 </when>
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575 <when value="paired_collection">
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576 <action type="format">
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577 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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578 </action>
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579 </when>
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580 </conditional>
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parents: 22
diff changeset
581 <expand macro="dbKeyActions" />
11
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582 </actions>
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583 </data>
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584 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
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585 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
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586 <actions>
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diff changeset
587 <conditional name="library.type">
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588 <when value="paired">
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589 <action type="format">
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590 <option type="from_param" name="library.input_2" param_attribute="ext" />
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591 </action>
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592 </when>
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593 <when value="paired_collection">
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parents: 10
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594 <action type="format">
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parents: 10
diff changeset
595 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 10
diff changeset
596 </action>
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597 </when>
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parents: 10
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598 </conditional>
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iuc
parents: 22
diff changeset
599 <expand macro="dbKeyActions" />
11
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parents: 10
diff changeset
600 </actions>
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601 </data>
0
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diff changeset
602 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
2a6cfe8997aa Uploaded from GH
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parents: 1
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603 <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
604 <actions>
5
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diff changeset
605 <conditional name="library.type">
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diff changeset
606 <when value="paired">
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607 <action type="format">
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parents: 2
diff changeset
608 <option type="from_param" name="library.input_2" param_attribute="ext" />
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parents: 2
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609 </action>
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diff changeset
610 </when>
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611 <when value="paired_collection">
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parents: 2
diff changeset
612 <action type="format">
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parents: 2
diff changeset
613 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 2
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614 </action>
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615 </when>
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616 </conditional>
23
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parents: 22
diff changeset
617 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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618 </actions>
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parents:
diff changeset
619 </data>
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parents: 23
diff changeset
620 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
22
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parents: 21
diff changeset
621 <change_format>
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parents: 21
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622 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
24
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parents: 23
diff changeset
623 <when input="sam_options.sam_opt" value="true" format="sam" />
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624 </change_format>
0
a03a7ee6cdff Imported from capsule None
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625 <actions>
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626 <conditional name="reference_genome.source">
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627 <when value="indexed">
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628 <action type="metadata" name="dbkey">
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629 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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630 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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631 <filter type="param_value" ref="reference_genome.index" column="0"/>
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632 </option>
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633 </action>
a03a7ee6cdff Imported from capsule None
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634 </when>
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635 <when value="history">
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636 <action type="metadata" name="dbkey">
a03a7ee6cdff Imported from capsule None
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637 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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parents:
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638 </action>
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639 </when>
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640 </conditional>
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diff changeset
641 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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642 </actions>
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643 </data>
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644 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
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645 <filter>save_mapping_stats is True</filter>
23
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parents: 22
diff changeset
646 <actions>
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parents: 22
diff changeset
647 <expand macro="dbKeyActions" />
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parents: 22
diff changeset
648 </actions>
10
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649 </data>
0
a03a7ee6cdff Imported from capsule None
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650 </outputs>
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651 <tests>
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parents: 23
diff changeset
652 <test expect_num_outputs="1">
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653 <!-- test on paired-end datasets -->
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parents: 1
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654 <param name="type" value="paired"/>
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parents: 1
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655 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
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656 <param name="unaligned_file" value="false"/>
2
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parents: 1
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657 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
658 <param name="source" value="history" />
2
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parents: 1
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659 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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parents: 1
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660 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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parents: 1
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661 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 1
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662 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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663 </test>
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parents: 24
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664 <test expect_num_outputs="3">
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parents: 24
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665 <!-- test on list paired collection -->
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parents: 16
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666 <param name="type" value="paired_collection"/>
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667 <param name="paired_options_selector" value="no"/>
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parents: 24
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668 <param name="unaligned_file" value="true"/>
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parents: 16
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669 <param name="analysis_type_selector" value="simple"/>
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parents: 16
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670 <param name="source" value="history" />
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parents: 16
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671 <param name="input_1">
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parents: 16
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672 <collection type="paired">
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parents: 16
diff changeset
673 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
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parents: 16
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674 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
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675 </collection>
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parents: 16
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676 </param>
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parents: 16
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677 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 16
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678 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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parents: 16
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679 </test>
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680 <test expect_num_outputs="1">
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681 <!-- test on paired-end datasets with read group info -->
5
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682 <param name="type" value="paired"/>
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683 <param name="paired_options_selector" value="no"/>
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684 <param name="unaligned_file" value="false"/>
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685 <param name="analysis_type_selector" value="simple"/>
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686 <param name="rg_selector" value="set"/>
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687 <param name="ID" value="rg1"/>
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688 <param name="PL" value="CAPILLARY"/>
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689 <param name="source" value="history" />
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690 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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691 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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692 <param name="own_file" value="bowtie2-ref.fasta" />
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693 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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694 </test>
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695 <test expect_num_outputs="2">
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parents: 16
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696 <!-- test on paired-end datasets with stats output -->
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697 <param name="type" value="paired"/>
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698 <param name="paired_options_selector" value="no"/>
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parents: 8
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699 <param name="unaligned_file" value="false"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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parents: 8
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700 <param name="analysis_type_selector" value="simple"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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diff changeset
701 <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
702 <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
703 <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
704 <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
705 <param name="save_mapping_stats" value="true" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
706 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
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iuc
parents: 14
diff changeset
707 <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
708 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
709 <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
710 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
711 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
712 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
713 <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
714 <!-- 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
715 <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
716 <!-- <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
717 <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
718 <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
719 <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
720 <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
721 <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
722 <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
723 <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
724 <param name="own_file" value="bowtie2-ref.fasta" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
725 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
726 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
727 <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
728 <!-- 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
729 <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
730 <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
731 <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
732 <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
733 <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
734 <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
735 <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
736 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
737 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
738 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
739 <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
740 <!-- 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
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 <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
748 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
749 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
750 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
751 <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
752 <!-- test on fasta paired-end datasets -->
16
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iuc
parents: 15
diff changeset
753 <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
754 <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
755 <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
756 <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
757 <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
758 <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
759 <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
760 <param name="own_file" value="bowtie2-ref.fasta" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
761 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
762 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
763 <test expect_num_outputs="1">
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
764 <!-- 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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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iuc
parents: 21
diff changeset
771 <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
772 <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
773 <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
774 <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
775 <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
776 </test>
24
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iuc
parents: 23
diff changeset
777 <test expect_num_outputs="1">
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
778 <!-- test on fasta paired-end datasets with sam as output -->
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
779 <param name="type" value="paired"/>
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
780 <param name="paired_options_selector" value="no"/>
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
781 <param name="unaligned_file" value="false"/>
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
782 <param name="analysis_type_selector" value="simple"/>
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
783 <param name="source" value="history" />
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784 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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785 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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786 <param name="own_file" value="bowtie2-ref.fasta" />
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787 <param name="sam_options_selector" value="yes" />
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788 <param name="sam_options|sam_opt" value="true" />
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789 <output name="output" ftype="sam">
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790 <assert_contents>
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791 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
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792 </assert_contents>
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793 </output>
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794 </test>
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a03a7ee6cdff Imported from capsule None
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795 </tests>
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796 <help><![CDATA[
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797 **Bowtie2 Overview**
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798
2
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799 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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800 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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801
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802 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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803 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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804 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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805
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806 -----
0
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807
2
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808 **Selecting reference genomes for Bowtie2**
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809
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810 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:
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811
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812 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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813 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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814
2
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815 If your genome of interest is not listed here you have two choices:
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816
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817 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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818 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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819
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820 ------
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821
2
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822 .. class:: infomark
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823
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824 **Bowtie2 options**
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825
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826 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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827
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828 -----
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829
0
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830 **Inputs**
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831
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832 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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833
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834 ------
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835
2
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836 **Input options**::
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837
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838 --interleaved
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839 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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840
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841 -s/--skip <int>
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842 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
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843
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844 -u/--qupto <int>
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845 Align the first `<int>` reads or read pairs from the input (after the
2
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846 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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847
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848 -5/--trim5 <int>
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849 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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850
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851 -3/--trim3 <int>
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852 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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853
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854 --phred33
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855 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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856 also called the "Phred+33" encoding, which is used by the very latest Illumina
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857 pipelines.
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858
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diff changeset
859 --phred64
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860 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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861 also called the "Phred+64" encoding.
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862
2
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863 --solexa-quals
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864 Convert input qualities from Solexa Phred quality (which can be negative) to
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865 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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866 Pipeline versions (prior to 1.3). Default: off.
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867
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868 --int-quals
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869 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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870 Integers are treated as being on the Phred quality scale unless
2
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871 `--solexa-quals` is also specified. Default: off.
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872
2
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873 ------
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874
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875 **Presets in `--end-to-end` mode**::
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876
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877 --very-fast
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878 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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879
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880 --fast
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881 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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882
2
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883 --sensitive
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884 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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885
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886 --very-sensitive
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887 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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888
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889 ------
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890
2
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891 **Presets options in `--local` mode**::
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892
2
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893 --very-fast-local
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894 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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895
2
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896 --fast-local
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897 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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898
2
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899 --sensitive-local
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900 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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901
2
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902 --very-sensitive-local
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903 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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904
0
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905 ------
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906
2
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907 **Alignment options**::
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908
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diff changeset
909 -N <int>
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910 Sets the number of mismatches to allowed in a seed alignment during multiseed
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911 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
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912 (often much slower) but increases sensitivity. Default: 0.
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913
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914 -L <int>
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915 Sets the length of the seed substrings to align during multiseed alignment.
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916 Smaller values make alignment slower but more sensitive. Default: the
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917 `--sensitive` preset is used by default, which sets `-L` to 22 in
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918 `--end-to-end` mode and to 20 in `--local` mode.
2
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919
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920 -i <func>
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921 Sets a function governing the interval between seed substrings to use during
5
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922 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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923 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
924
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diff changeset
925 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
926 Seed 1 fw: TAGCTACGCT
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diff changeset
927 Seed 1 rc: AGCGTAGCTA
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diff changeset
928 Seed 2 fw: CGCTCTACGC
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diff changeset
929 Seed 2 rc: GCGTAGAGCG
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930 Seed 3 fw: ACGCTATCAT
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diff changeset
931 Seed 3 rc: ATGATAGCGT
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diff changeset
932 Seed 4 fw: TCATGCATAA
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diff changeset
933 Seed 4 rc: TTATGCATGA
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diff changeset
934
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diff changeset
935 Since it's best to use longer intervals for longer reads, this parameter sets
2a6cfe8997aa Uploaded from GH
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diff changeset
936 the interval as a function of the read length, rather than a single
2a6cfe8997aa Uploaded from GH
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diff changeset
937 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
938 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
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parents: 2
diff changeset
939 If the function returns a result less than
2
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diff changeset
940 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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diff changeset
941 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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diff changeset
942 in `--local` mode.
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943
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diff changeset
944 --n-ceil <func>
2
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parents: 1
diff changeset
945 Sets a function governing the maximum number of ambiguous characters (usually
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
946 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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diff changeset
947 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
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parents: 2
diff changeset
948 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
949 Default: `L,0,0.15`.
2
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950
11
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diff changeset
951 --dpad <int>
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diff changeset
952 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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diff changeset
953 gaps. Default: 15.
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954
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diff changeset
955 --gbar <int>
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diff changeset
956 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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957 Default: 4.
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958
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959 --ignore-quals
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960 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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diff changeset
961 mismatched position to be the highest possible, regardless of the actual value.
2
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962 I.e. input is treated as though all quality values are high. This is also the
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963 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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964 `-r`, or `-c` modes).
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965
2
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966 --nofw/--norc
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967 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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968 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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969 not attempt to align unpaired reads against the reverse-complement (Crick)
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970 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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971 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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972 paired-end configurations corresponding to fragments from the reverse-complement
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diff changeset
973 (Crick) strand. Default: both strands enabled.
2
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974
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975 --no-1mm-upfront
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976 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
5
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977 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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978 alignments can be found very quickly, and many short read alignments have exact or
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979 near-exact end-to-end alignments. However, this can lead to unexpected
5
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diff changeset
980 alignments when the user also sets options governing the multiseed heuristic,
2
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981 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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982 to the length of the read, the user will be surprised to find 1-mismatch alignments
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983 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
5
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diff changeset
984 alignments before using the multiseed heuristic, which leads to the expected
2
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985 behavior when combined with options such as `-L` and `-N`. This comes at the
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986 expense of speed.
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987
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988 --end-to-end
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989 In this mode, Bowtie 2 requires that the entire read align from one end to the
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990 other, without any trimming (or "soft clipping") of characters from either end.
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991 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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992 are less than or equal to 0, and the greatest possible alignment score is 0.
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993 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
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994
2
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995 --local
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996 In this mode, Bowtie 2 does not require that the entire read align from one end
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997 to the other. Rather, some characters may be omitted ("soft clipped") from the
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998 ends in order to achieve the greatest possible alignment score. The match bonus
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diff changeset
999 `--ma` is used in this mode, and the best possible alignment score is equal to
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1000 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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1001 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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1002 the local version of the preset (`--very-fast-local`). This is mutually
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1003 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1004
2
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1005 -----
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1006
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diff changeset
1007 **Scoring options**::
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1008
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diff changeset
1009 --ma <int>
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diff changeset
1010 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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1011 score for each position where a read character aligns to a reference character
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1012 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1013
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diff changeset
1014 --mp MX,MN
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1015 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1016 number less than or equal to `MX` and greater than or equal to `MN` is
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1017 subtracted from the alignment score for each position where a read character
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1018 aligns to a reference character, the characters do not match, and neither is an
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1019 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1020 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1021 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1022
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diff changeset
1023 --np <int>
2
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1024 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1025 ambiguous character such as `N`. Default: 1.
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1026
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1027 --rdg <int1>,<int2>
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1028 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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diff changeset
1029 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1030
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1031 --rfg <int1>,<int2>
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1032 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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1033 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1034 5, 3.
0
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1035
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diff changeset
1036 --score-min <func>
2
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1037 Sets a function governing the minimum alignment score needed for an alignment to
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1038 be considered "valid" (i.e. good enough to report). This is a function of read
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1039 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
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1040 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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1041 the default in `--local` mode is `G,20,8`.
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1042
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1043 -----
2
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1044
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1045 **Reporting options**::
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1046
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diff changeset
1047 -k <int>
2
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1048 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1049 When it finds a valid alignment, it continues looking for alignments that are
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1050 nearly as good or better. The best alignment found is reported (randomly
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1051 selected from among best if tied). Information about the best alignments is
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1052 used to estimate mapping quality and to set SAM optional fields, such as
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1053 `AS:i` and `XS:i`.
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1054
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1055 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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1056 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1057 search terminates when it can't find more distinct valid alignments, or when it
11
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1058 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1059 descending order by alignment score. The alignment score for a paired-end
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1060 alignment equals the sum of the alignment scores of the individual mates. Each
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1061 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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1062 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1063 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
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1064 `<int>` alignments reported are the best possible in terms of alignment score.
2
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1065 `-k` is mutually exclusive with `-a`.
0
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1066
2
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diff changeset
1067 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
1068 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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diff changeset
1069
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diff changeset
1070 -a
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diff changeset
1071 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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diff changeset
1072 is mutually exclusive with `-k`.
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diff changeset
1073
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diff changeset
1074 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1075 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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diff changeset
1076
2
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diff changeset
1077 -----
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diff changeset
1078
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diff changeset
1079 **Effort options**::
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diff changeset
1080
11
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diff changeset
1081 -D <int>
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diff changeset
1082 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
2a6cfe8997aa Uploaded from GH
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diff changeset
1083 moves on, using the alignments found so far. A seed extension "fails" if it
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parents: 1
diff changeset
1084 does not yield a new best or a new second-best alignment. This limit is
2a6cfe8997aa Uploaded from GH
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diff changeset
1085 automatically adjusted up when -k or -a are specified. Default: 15.
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diff changeset
1086
11
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diff changeset
1087 -R <int>
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diff changeset
1088 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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parents: 1
diff changeset
1089 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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parents: 1
diff changeset
1090 (same length, same number of mismatches allowed) at different offsets and
2a6cfe8997aa Uploaded from GH
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diff changeset
1091 searches for more alignments. A read is considered to have repetitive seeds if
2a6cfe8997aa Uploaded from GH
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diff changeset
1092 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
1093 least once is greater than 300. Default: 2.
11
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diff changeset
1094
2
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diff changeset
1095 -----
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diff changeset
1096
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diff changeset
1097 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1098
11
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diff changeset
1099 -I/--minins <int>
2
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1100 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
2a6cfe8997aa Uploaded from GH
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parents: 1
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1101 specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1102 appropriate orientation with a 20-bp gap between them, that alignment is
2a6cfe8997aa Uploaded from GH
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1103 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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parents: 1
diff changeset
1104 be valid in that case. If trimming options `-3` or `-5` are also used, the
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1105 `-I` constraint is applied with respect to the untrimmed mates.
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1106
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diff changeset
1107 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1108 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1109 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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parents: 1
diff changeset
1110 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1111 efficient.
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diff changeset
1112
11
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diff changeset
1113 Default: 0 (essentially imposing no minimum)
2
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1114
11
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diff changeset
1115 -X/--maxins <int>
2
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diff changeset
1116 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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parents: 1
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1117 is specified and a paired-end alignment consists of two 20-bp alignments in the
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parents: 1
diff changeset
1118 proper orientation with a 60-bp gap between them, that alignment is considered
2a6cfe8997aa Uploaded from GH
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diff changeset
1119 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
1120 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1121 constraint is applied with respect to the untrimmed mates, not the trimmed
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1122 mates.
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diff changeset
1123
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1124 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1125 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1126 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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parents: 1
diff changeset
1127 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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diff changeset
1128 efficient.
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1129
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1130 Default: 500.
0
a03a7ee6cdff Imported from capsule None
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1131
2
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diff changeset
1132 --fr/--rf/--ff
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1133 The upstream/downstream mate orientations for a valid paired-end alignment
2a6cfe8997aa Uploaded from GH
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1134 against the forward reference strand. E.g., if `--fr` is specified and there is
2a6cfe8997aa Uploaded from GH
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diff changeset
1135 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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diff changeset
1136 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
2a6cfe8997aa Uploaded from GH
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1137 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1138 complement of mate 1 and all other constraints are met, that too is valid.
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1139 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1140 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1141 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1142 for Illumina's Paired-end Sequencing Assay).
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diff changeset
1143
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1144 --no-mixed
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1145 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1146 a pair, it then tries to find alignments for the individual mates. This option
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diff changeset
1147 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1148
2
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1149 --no-discordant
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1150 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1151 concordant alignments. A discordant alignment is an alignment where both mates
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1152 align uniquely, but that does not satisfy the paired-end constraints
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1153 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1154
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1155 --dovetail
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1156 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
1157 beginning of the other such that the wrong mate begins upstream, consider that
5
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diff changeset
1158 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1159
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1160 --no-contain
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1161 If one mate alignment contains the other, consider that to be non-concordant.
5
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1162 Default: a mate can contain the other in a concordant alignment.
2
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1163
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1164 --no-overlap
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1165 If one mate alignment overlaps the other at all, consider that to be
5
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diff changeset
1166 non-concordant. Default: mates can overlap in a concordant alignment.
11
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1167
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1168 ------
a03a7ee6cdff Imported from capsule None
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1169
2
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diff changeset
1170 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
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1171
11
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diff changeset
1172 --rg-id <text>
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diff changeset
1173 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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diff changeset
1174 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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diff changeset
1175 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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diff changeset
1176 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1177
11
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diff changeset
1178 --rg <text>
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diff changeset
1179 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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1180 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
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diff changeset
1181 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1182 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1183 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1184
2
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diff changeset
1185 --omit-sec-seq
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diff changeset
1186 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1187 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1188 in those fields instead.
11
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1189
2
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1190 -----
0
a03a7ee6cdff Imported from capsule None
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parents:
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1191
2
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diff changeset
1192 **Other options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1193
2
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1194 --reorder
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1195 Guarantees that output SAM records are printed in an order corresponding to the
2a6cfe8997aa Uploaded from GH
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1196 order of the reads in the original input file, even when `-p` is set greater
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1197 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1198 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1199 not specified. Has no effect if `-p` is set to 1, since output order will
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1200 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
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1201
11
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1202 --seed <int>
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1203 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
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1204
2
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diff changeset
1205 --non-deterministic
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1206 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1207 seeds the generator with a number derived from (a) the read name, (b) the
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1208 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1209 option. This means that if two reads are identical (same name, same
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1210 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1211 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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diff changeset
1212 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1213 current time. This means that Bowtie 2 will not necessarily report the same
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diff changeset
1214 alignment for two identical reads. This is counter-intuitive for some users,
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1215 but might be more appropriate in situations where the input consists of many
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diff changeset
1216 identical reads.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1217
15
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1218 -----
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iuc
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diff changeset
1219
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diff changeset
1220
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1221 **Paired-end (and mate-pair) data in fastq format**
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1222
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1223 Paired end datasets can be represented as two individual datasets:
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1224
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1225 First dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1226
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1227 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1228 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1229 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1230 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
1231 @2/1
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diff changeset
1232 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1233 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1234 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1235
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diff changeset
1236 Second dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1237
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1238 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1239 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1240 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1241 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
1242 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1243 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1244 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1245 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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diff changeset
1246
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diff changeset
1247 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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diff changeset
1248
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diff changeset
1249 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1250 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1251 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1252 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1253 @1/2
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diff changeset
1254 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1255 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1256 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
1257 @2/1
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diff changeset
1258 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1259 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1260 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1261 @2/2
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diff changeset
1262 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1263 +
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1264 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
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diff changeset
1265 ]]></help>
2
2a6cfe8997aa Uploaded from GH
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1266 <citations>
17
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diff changeset
1267 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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diff changeset
1268 <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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diff changeset
1269 </citations>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1270 </tool>