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annotate bowtie2_wrapper.xml @ 31:f66e4858ca26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
author iuc
date Wed, 06 Jul 2022 10:24:52 +0000
parents 2f3400246bfc
children 6b4916819621
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31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
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1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2
2a6cfe8997aa Uploaded from GH
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2 <description>- map reads against reference genome</description>
31
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3 <macros>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
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4 <import>bowtie2_macros.xml</import>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
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5 </macros>
29
56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <xrefs>
56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <xref type="bio.tools">bowtie2</xref>
56dcf3929d02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 </xrefs>
11
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9 <requirements>
27
c9105910063f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
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10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
30
2f3400246bfc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
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11 <requirement type="package" version="1.14">samtools</requirement>
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12 </requirements>
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a03a7ee6cdff Imported from capsule None
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13 <version_command>bowtie2 --version</version_command>
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14 <command detect_errors="exit_code"><![CDATA[
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15 ## Use pipefail if available to quit with first non-zero exit code
e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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16 set -o | grep -q pipefail && set -o pipefail;
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17 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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18 #set index_path = ''
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19 #if str($reference_genome.source) == "history":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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20 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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21 ln -s -f '$reference_genome.own_file' genome.fa &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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22 #set index_path = 'genome'
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23 #else:
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24 #set index_path = $reference_genome.index.fields.path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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25 #end if
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27 ## Link in the input files, so bowtie2 can tell their type
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29 #set compressed="False"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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30 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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31 #if str($library.type) == 'paired':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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32 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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33 #set read1 = "input_f.fastq.gz"
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34 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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35 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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37 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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38 #else if $library.input_1.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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39 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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40 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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42 #set read1 = "input_f.fastq"
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43 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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44 ln -f -s '${library.input_1}' ${read1} &&
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45
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46 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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47 #set read2 = "input_r.fastq.gz"
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48 #set compressed = "GZ"
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49 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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50 #set read2 = "input_r.fastq.bz2"
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51 #set compressed = "BZ2"
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52 #else if $library.input_2.is_of_type('fasta'):
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53 #set read2 = "input_r.fasta"
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54 #else:
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55 #set read2 = "input_r.fastq"
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56 #end if
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57 ln -f -s '${library.input_2}' ${read2} &&
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58 #else if str($library.type) == 'paired_collection':
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59 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 #set read1 = "input_f.fastq.gz"
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61 #set compressed = "GZ"
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62 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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63 #set read1 = "input_f.fastq.bz2"
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64 #set compressed = "BZ2"
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65 #else if $library.input_1.forward.is_of_type('fasta'):
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66 #set reads_are_fastq = False
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67 #set read1 = "input_f.fasta"
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68 #else:
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69 #set read1 = "input_f.fastq"
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70 #end if
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71 ln -s '${library.input_1.forward}' ${read1} &&
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73 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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74 #set read2 = "input_r.fastq.gz"
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75 #set compressed = "GZ"
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76 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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77 #set read2 = "input_r.fastq.bz2"
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78 #set compressed = "BZ2"
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79 #else if $library.input_1.reverse.is_of_type("fasta"):
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80 #set read2 = "input_r.fasta"
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81 #else:
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82 #set read2 = "input_r.fastq"
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83 #end if
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84 ln -s '${library.input_1.reverse}' ${read2} &&
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85
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86 #else if str($library.type) == 'paired_interleaved':
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87 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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88 #set read1 = "input_il.fastq.gz"
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89 #set compressed = "GZ"
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90 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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91 #set read1 = "input_il.fastq.bz2"
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92 #set compressed = "BZ2"
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93 #else if $library.input_1.is_of_type("fasta"):
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94 #set reads_are_fastq = False
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95 #set read1 = "input_il.fasta"
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96 #else:
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97 #set read1 = "input_il.fastq"
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98 #end if
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99 ln -s '${library.input_1}' ${read1} &&
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100 #else:
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101 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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102 #set read1 = "input_f.fastq.gz"
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103 #set compressed = "GZ"
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104 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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iuc
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105 #set read1 = "input_f.fastq.bz2"
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106 #set compressed = "BZ2"
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107 #else if $library.input_1.is_of_type("fasta"):
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108 #set reads_are_fastq = False
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109 #set read1 = "input_f.fasta"
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110 #else:
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111 #set read1 = "input_f.fastq"
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112 #end if
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113 ln -s '${library.input_1}' ${read1} &&
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114 #end if
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115
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116 ## execute bowtie2
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117
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118 bowtie2
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119
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120 ## number of threads
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121 -p \${GALAXY_SLOTS:-4}
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122
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123 ## index file path
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124 -x '$index_path'
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125
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126 ## Input reads are fasta?
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127 #if not reads_are_fastq:
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128 -f
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129 #end if
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130
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131 ## Input reads
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132 #if str( $library.type ) == "single":
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133 -U '${read1}'
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134 #if str( $library.unaligned_file ) == "true":
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135 #if $compressed == "GZ":
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136 --un-gz '${output_unaligned_reads_l}'
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137 #else if $compressed == "BZ2":
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138 --un-bz2 '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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139 #else:
18
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140 --un '${output_unaligned_reads_l}'
14
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141 #end if
18
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142 #end if
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143 #if str( $library.aligned_file ) == "true":
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144 #if $compressed == "GZ":
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145 --al-gz '${output_aligned_reads_l}'
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146 #else if $compressed == "BZ2":
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147 --al-bz2 '${output_aligned_reads_l}'
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148 #else:
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149 --al '${output_aligned_reads_l}'
16
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150 #end if
18
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151 #end if
15
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152
18
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153 #elif str( $library.type ) == "paired_interleaved":
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154 --interleaved '${read1}'
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155 #if str( $library.unaligned_file ) == "true":
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156 #if $compressed == "GZ":
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157 --un-gz '${output_unaligned_reads_l}'
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158 #else if $compressed == "BZ2":
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159 --un-bz2 '${output_unaligned_reads_l}'
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160 #else:
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161 --un '${output_unaligned_reads_l}'
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162 #end if
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163 #end if
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164 #if str( $library.aligned_file ) == "true":
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165 #if $compressed == "GZ":
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diff changeset
166 --al-gz '${output_aligned_reads_l}'
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167 #else if $compressed == "BZ2":
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168 --al-bz2 '${output_aligned_reads_l}'
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169 #else:
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170 --al '${output_aligned_reads_l}'
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171 #end if
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172 #end if
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173 #else:
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174 -1 '${read1}'
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175 -2 '${read2}'
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176 #if str( $library.unaligned_file ) == "true":
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177 #if $compressed == "GZ":
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178 --un-conc-gz '${output_unaligned_reads_l}'
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179 #else if $compressed == "BZ2":
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180 --un-conc-bz2 '${output_unaligned_reads_l}'
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181 #else:
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182 --un-conc '${output_unaligned_reads_l}'
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183 #end if
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184 #end if
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185 #if str( $library.aligned_file ) == "true":
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186 #if $compressed == "GZ":
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187 --al-conc-gz '${output_aligned_reads_l}'
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188 #else if $compressed == "BZ2":
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189 --al-conc-bz2 '${output_aligned_reads_l}'
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190 #else:
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191 --al-conc '${output_aligned_reads_l}'
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192 #end if
18
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193 #end if
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194 #if str( $library.paired_options.paired_options_selector ) == "yes":
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195 -I ${library.paired_options.I}
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196 -X ${library.paired_options.X}
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197 ${library.paired_options.fr_rf_ff}
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198 ${library.paired_options.no_mixed}
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199 ${library.paired_options.no_discordant}
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200 ${library.paired_options.dovetail}
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201 ${library.paired_options.no_contain}
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202 ${library.paired_options.no_overlap}
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203 #end if
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204 #end if
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205
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206 ## Read group information.
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207 @define_read_group_helpers@
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208 #if str( $library.type ) == "single":
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209 #set $rg_auto_name = $read_group_name_default($library.input_1)
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210 #elif str( $library.type ) == "paired":
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211 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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212 #else
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213 #set $rg_auto_name = $read_group_name_default($library.input_1)
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214 #end if
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215 @set_use_rg_var@
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216 @set_read_group_vars@
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217 #if $use_rg
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218 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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219 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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220 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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221 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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222 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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223 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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224 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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225 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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226 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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227 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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228 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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229 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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230 #end if
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231
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232 ## Analysis type
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233 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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234 $analysis_type.presets
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235 #elif str( $analysis_type.analysis_type_selector ) == "full":
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236 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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237 --skip ${analysis_type.input_options.skip}
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238 --qupto ${analysis_type.input_options.qupto}
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239 --trim5 ${analysis_type.input_options.trim5}
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240 --trim3 ${analysis_type.input_options.trim3}
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241 ${analysis_type.input_options.qv_encoding}
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242 ${analysis_type.input_options.solexa_quals}
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243 ${analysis_type.input_options.int_quals}
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244 #end if
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245
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246 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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247 -N ${analysis_type.alignment_options.N}
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248 -L ${analysis_type.alignment_options.L}
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249 -i '${analysis_type.alignment_options.i}'
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250 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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251 --dpad ${analysis_type.alignment_options.dpad}
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252 --gbar ${analysis_type.alignment_options.gbar}
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253 ${analysis_type.alignment_options.ignore_quals}
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254 ${analysis_type.alignment_options.nofw}
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255 ${analysis_type.alignment_options.norc}
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256 ${analysis_type.alignment_options.no_1mm_upfront}
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257 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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258 --end-to-end
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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260 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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261 --local
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262 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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263 #end if
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264 #end if
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265
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266 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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267 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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268 --ma ${analysis_type.scoring_options.ma}
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269 #end if
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270 --mp '${analysis_type.scoring_options.mp}'
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271 --np ${analysis_type.scoring_options.np}
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272 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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273 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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274 #end if
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275
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276 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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277 -k ${analysis_type.reporting_options.k}
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278 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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279 -a
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280 #end if
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281
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282 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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283 -D ${analysis_type.effort_options.D}
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284 -R ${analysis_type.effort_options.R}
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285 #end if
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286 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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287 ${analysis_type.other_options.non_deterministic}
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288 --seed ${analysis_type.other_options.seed}
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289 #end if
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290
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291 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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292 ${analysis_type.cline}
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293 #end if
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294
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295 #if str( $sam_options.sam_options_selector ) == "yes":
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296 ${sam_options.no_unal}
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297 ${sam_options.omit_sec_seq}
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298 ${sam_options.sam_no_qname_trunc}
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299 ${sam_options.xeq}
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300 ${sam_options.soft_clipped_unmapped_tlen}
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301 ${sam_options.reorder}
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302 #end if
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303
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304 ## mapping stats (i.e. stderr from bowtie2)
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305 #if $save_mapping_stats
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306 2> '$mapping_stats'
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307 #end if
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308
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309 ## output file
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310 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
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311 | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
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312 #else if $sam_options.reorder:
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313 | samtools view --no-PG -bS - -o '$output'
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314 #else:
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315 > '$output'
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316 #end if
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317
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318 ## rename unaligned sequence files
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319 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
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320 #from os.path import splitext
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321 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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322 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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323 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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324 #end if
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325 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
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326 #from os.path import splitext
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327 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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328 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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329 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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330 #end if
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331
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332 ]]></command>
0
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333 <inputs>
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334 <!-- single/paired -->
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335 <conditional name="library">
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336 <param name="type" type="select" label="Is this single or paired library">
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337 <option value="single">Single-end</option>
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338 <option value="paired">Paired-end</option>
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339 <option value="paired_collection">Paired-end Dataset Collection</option>
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340 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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341 </param>
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342
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343 <when value="single">
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344 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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345 <expand macro="align_unalign" />
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346 </when>
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347 <when value="paired">
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348 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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349 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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350 <expand macro="align_unalign" />
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351 <expand macro="paired_end_options" />
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352 </when>
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353 <when value="paired_collection">
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354 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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355 <expand macro="align_unalign" />
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356 <expand macro="paired_end_options" />
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357 </when>
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358 <when value="paired_interleaved">
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359 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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360 <expand macro="align_unalign" />
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361 <expand macro="paired_end_options" />
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362 </when>
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363 </conditional>
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364 <!-- reference genome -->
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365 <conditional name="reference_genome">
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366 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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367 <option value="indexed">Use a built-in genome index</option>
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368 <option value="history">Use a genome from the history and build index</option>
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369 </param>
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370 <when value="indexed">
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371 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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372 <options from_data_table="bowtie2_indexes">
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373 <filter type="sort_by" column="2"/>
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374 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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375 </options>
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376 </param>
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377 </when>
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378 <when value="history">
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379 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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380 </when>
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381 </conditional>
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382 <!-- read group settings -->
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383 <expand macro="read_group_conditional" />
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384 <conditional name="analysis_type">
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385 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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386 <option value="simple">1: Default setting only</option>
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387 <option value="full">2: Full parameter list</option>
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388 </param>
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389 <when value="simple">
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390 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
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391 <option value="no_presets" selected="True">No, just use defaults</option>
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392 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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393 <option value="--fast">Fast end-to-end (--fast)</option>
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394 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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395 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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396 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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397 <option value="--fast-local">Fast local (--fast-local)</option>
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398 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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399 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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400 </param>
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401 </when>
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402 <when value="full">
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403 <conditional name="input_options">
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404 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
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405 <option value="yes">Yes</option>
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406 <option value="no" selected="true">No</option>
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407 </param>
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408 <when value="yes">
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409 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
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410 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
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411 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
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412 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
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413 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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414 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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415 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
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416 </param>
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417 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
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418 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
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419 </when>
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420 <when value="no">
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421 <!-- do nothing -->
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422 </when>
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423 </conditional>
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424 <conditional name="alignment_options">
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425 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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426 <option value="yes">Yes</option>
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427 <option value="no" selected="true">No</option>
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428 </param>
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429 <when value="yes">
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430 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
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431 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
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432 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
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433 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
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434 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
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435 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
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436 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
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437 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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438 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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439 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
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440 <conditional name="align_mode">
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441 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
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442 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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443 <option value="local">Local (--local)</option>
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444 </param>
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445 <when value="end-to-end">
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446 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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447 </when>
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448 <when value="local">
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449 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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450 </when>
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451 </conditional>
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452 </when>
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453 <when value="no">
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454 <!-- do nothing -->
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455 </when>
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456 </conditional>
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457 <conditional name="scoring_options">
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458 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
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459 <option value="yes">Yes</option>
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460 <option value="no" selected="true">No</option>
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461 </param>
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462 <when value="yes">
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463 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
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464 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
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465 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
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466 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
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467 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
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468 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
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469 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
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470 </when>
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471 <when value="no">
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472 <!-- do nothing -->
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473 </when>
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474 </conditional>
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475 <conditional name="reporting_options">
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476 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
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477 <option value="no" selected="true">No, do not set</option>
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478 <option value="k">Set -k option and enter -k value</option>
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479 <option value="a">Set -a option</option>
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480 </param>
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481 <when value="no">
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482 <!-- do nothing -->
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483 </when>
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484 <when value="k">
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485 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
2
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486 </when>
5
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487 <when value="a">
2
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488 <!-- do nothing here; set -a flag on the command line-->
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489 </when>
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490 </conditional>
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491 <conditional name="effort_options">
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492 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
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493 <option value="yes">Yes</option>
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494 <option value="no" selected="true">No</option>
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495 </param>
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496 <when value="yes">
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497 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
2
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498 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
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499 </when>
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500 <when value="no">
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501 <!-- do nothing -->
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502 </when>
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503 </conditional>
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504 <conditional name="other_options">
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505 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
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506 <option value="yes">Yes</option>
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507 <option value="no" selected="true">No</option>
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508 </param>
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509 <when value="yes">
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510 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
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511 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
2
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512 </when>
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513 <when value="no">
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514 <!-- do nothing -->
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515 </when>
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516 </conditional>
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517 </when>
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518 </conditional>
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519 <conditional name="sam_options">
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520 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
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521 <option value="yes">Yes</option>
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522 <option value="no" selected="true">No</option>
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523 </param>
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524 <when value="yes">
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525 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
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526 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
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527 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
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528 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
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529 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
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530 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
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531 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
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532 label="Reorder output to reflect order of the input file"
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533 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
0
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534 </when>
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535 <when value="no"/>
0
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536 </conditional>
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537 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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538 </inputs>
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539 <!-- define outputs -->
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540 <outputs>
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541 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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542 <filter>library['unaligned_file'] is True</filter>
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543 <actions>
5
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544 <conditional name="library.type">
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545 <when value="single">
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546 <action type="format">
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547 <option type="from_param" name="library.input_1" param_attribute="ext" />
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548 </action>
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549 </when>
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550 <when value="paired">
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551 <action type="format">
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552 <option type="from_param" name="library.input_1" param_attribute="ext" />
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553 </action>
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554 </when>
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555 <when value="paired_collection">
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556 <action type="format">
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557 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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558 </action>
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559 </when>
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560 </conditional>
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561 <expand macro="dbKeyActions" />
0
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562 </actions>
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563 </data>
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564 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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565 <filter>library['aligned_file'] is True</filter>
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566 <actions>
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567 <conditional name="library.type">
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568 <when value="single">
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569 <action type="format">
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570 <option type="from_param" name="library.input_1" param_attribute="ext" />
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571 </action>
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572 </when>
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573 <when value="paired">
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574 <action type="format">
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575 <option type="from_param" name="library.input_1" param_attribute="ext" />
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576 </action>
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577 </when>
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578 <when value="paired_collection">
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579 <action type="format">
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580 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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581 </action>
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582 </when>
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583 </conditional>
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parents: 22
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584 <expand macro="dbKeyActions" />
11
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585 </actions>
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586 </data>
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587 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
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588 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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589 <actions>
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diff changeset
590 <conditional name="library.type">
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parents: 10
diff changeset
591 <when value="paired">
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parents: 10
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592 <action type="format">
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593 <option type="from_param" name="library.input_2" param_attribute="ext" />
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parents: 10
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594 </action>
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595 </when>
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596 <when value="paired_collection">
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parents: 10
diff changeset
597 <action type="format">
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parents: 10
diff changeset
598 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 10
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599 </action>
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parents: 10
diff changeset
600 </when>
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601 </conditional>
23
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iuc
parents: 22
diff changeset
602 <expand macro="dbKeyActions" />
11
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parents: 10
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603 </actions>
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parents: 10
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604 </data>
0
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605 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
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parents: 1
diff changeset
606 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
607 <actions>
5
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parents: 2
diff changeset
608 <conditional name="library.type">
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609 <when value="paired">
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parents: 2
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610 <action type="format">
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parents: 2
diff changeset
611 <option type="from_param" name="library.input_2" param_attribute="ext" />
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612 </action>
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613 </when>
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parents: 2
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614 <when value="paired_collection">
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615 <action type="format">
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diff changeset
616 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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parents: 2
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617 </action>
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618 </when>
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diff changeset
619 </conditional>
23
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parents: 22
diff changeset
620 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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621 </actions>
a03a7ee6cdff Imported from capsule None
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622 </data>
24
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parents: 23
diff changeset
623 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
22
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iuc
parents: 21
diff changeset
624 <change_format>
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parents: 21
diff changeset
625 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
24
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parents: 23
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626 <when input="sam_options.sam_opt" value="true" format="sam" />
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627 </change_format>
0
a03a7ee6cdff Imported from capsule None
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628 <actions>
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629 <conditional name="reference_genome.source">
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630 <when value="indexed">
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631 <action type="metadata" name="dbkey">
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632 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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633 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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634 <filter type="param_value" ref="reference_genome.index" column="0"/>
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635 </option>
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636 </action>
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637 </when>
a03a7ee6cdff Imported from capsule None
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638 <when value="history">
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639 <action type="metadata" name="dbkey">
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640 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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641 </action>
a03a7ee6cdff Imported from capsule None
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642 </when>
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643 </conditional>
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parents: 22
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644 <expand macro="dbKeyActions" />
0
a03a7ee6cdff Imported from capsule None
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645 </actions>
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646 </data>
10
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parents: 8
diff changeset
647 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
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diff changeset
648 <filter>save_mapping_stats is True</filter>
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parents: 22
diff changeset
649 <actions>
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iuc
parents: 22
diff changeset
650 <expand macro="dbKeyActions" />
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parents: 22
diff changeset
651 </actions>
10
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652 </data>
0
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653 </outputs>
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654 <tests>
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655 <test expect_num_outputs="1">
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656 <!-- test on paired-end datasets -->
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parents: 1
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657 <param name="type" value="paired"/>
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658 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
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659 <param name="unaligned_file" value="false"/>
2
2a6cfe8997aa Uploaded from GH
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parents: 1
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660 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
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661 <param name="source" value="history" />
2
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parents: 1
diff changeset
662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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parents: 1
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663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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parents: 1
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664 <param name="own_file" value="bowtie2-ref.fasta" />
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665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
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parents: 30
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666 <metadata name="sort_order" value="coordinate"/>
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parents: 30
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667 </output>
0
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668 </test>
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parents: 24
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669 <test expect_num_outputs="3">
739b008acace "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"
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parents: 24
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670 <!-- test on list paired collection -->
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parents: 16
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671 <param name="type" value="paired_collection"/>
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672 <param name="paired_options_selector" value="no"/>
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parents: 24
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673 <param name="unaligned_file" value="true"/>
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parents: 16
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674 <param name="analysis_type_selector" value="simple"/>
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parents: 16
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675 <param name="source" value="history" />
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parents: 16
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676 <param name="input_1">
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parents: 16
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677 <collection type="paired">
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parents: 16
diff changeset
678 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
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parents: 16
diff changeset
679 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
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parents: 16
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680 </collection>
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parents: 16
diff changeset
681 </param>
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parents: 16
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682 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 30
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683 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
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parents: 30
diff changeset
684 <metadata name="sort_order" value="coordinate"/>
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parents: 30
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685 </output>
17
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parents: 16
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686 </test>
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parents: 23
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687 <test expect_num_outputs="1">
17
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parents: 16
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688 <!-- test on paired-end datasets with read group info -->
5
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689 <param name="type" value="paired"/>
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690 <param name="paired_options_selector" value="no"/>
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691 <param name="unaligned_file" value="false"/>
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692 <param name="analysis_type_selector" value="simple"/>
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693 <param name="rg_selector" value="set"/>
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694 <param name="ID" value="rg1"/>
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695 <param name="PL" value="CAPILLARY"/>
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696 <param name="source" value="history" />
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697 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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diff changeset
698 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
699 <param name="own_file" value="bowtie2-ref.fasta" />
31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
700 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
701 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
702 </output>
5
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devteam
parents: 2
diff changeset
703 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
704 <test expect_num_outputs="2">
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
705 <!-- test on paired-end datasets with stats output -->
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
706 <param name="type" value="paired"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
707 <param name="paired_options_selector" value="no"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
708 <param name="unaligned_file" value="false"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
709 <param name="analysis_type_selector" value="simple"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
710 <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
711 <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
712 <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
713 <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
714 <param name="save_mapping_stats" value="true" />
31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
715 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
716 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
717 </output>
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
718 <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
719 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
720 <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
721 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 </test>
24
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
724 <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
725 <!-- 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
726 <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
727 <!-- <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
728 <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
729 <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
730 <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
731 <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
732 <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
733 <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
734 <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
735 <param name="own_file" value="bowtie2-ref.fasta" />
31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
736 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
737 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
738 </output>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
739 </test>
24
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iuc
parents: 23
diff changeset
740 <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
741 <!-- 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
742 <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
743 <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
744 <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
745 <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
746 <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
747 <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
748 <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
749 <param name="own_file" value="bowtie2-ref.fasta" />
31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
750 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
751 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
752 </output>
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 </test>
24
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iuc
parents: 23
diff changeset
754 <test expect_num_outputs="1">
17
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iuc
parents: 16
diff changeset
755 <!-- 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
756 <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
757 <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
758 <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
759 <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
760 <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
761 <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
762 <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
763 <param name="own_file" value="bowtie2-ref.fasta" />
31
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
764 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
765 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
766 </output>
14
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devteam
parents: 13
diff changeset
767 </test>
24
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iuc
parents: 23
diff changeset
768 <test expect_num_outputs="1">
17
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iuc
parents: 16
diff changeset
769 <!-- test on fasta paired-end datasets -->
16
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parents: 15
diff changeset
770 <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
771 <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
772 <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
773 <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
774 <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
775 <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
776 <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
777 <param name="own_file" value="bowtie2-ref.fasta" />
31
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iuc
parents: 30
diff changeset
778 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true">
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
779 <metadata name="sort_order" value="coordinate"/>
f66e4858ca26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 30
diff changeset
780 </output>
16
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iuc
parents: 15
diff changeset
781 </test>
24
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iuc
parents: 23
diff changeset
782 <test expect_num_outputs="1">
22
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iuc
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diff changeset
783 <!-- test on fasta paired-end datasets with bam_native as output -->
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diff changeset
784 <param name="type" value="paired"/>
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diff changeset
785 <param name="paired_options_selector" value="no"/>
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diff changeset
786 <param name="unaligned_file" value="false"/>
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diff changeset
787 <param name="analysis_type_selector" value="simple"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
788 <param name="source" value="history" />
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diff changeset
789 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
790 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
791 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
792 <param name="sam_options_selector" value="yes" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
793 <param name="reorder" value="true" />
31
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diff changeset
794 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">
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diff changeset
795 <metadata name="sort_order" value="unsorted"/>
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diff changeset
796 </output>
22
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diff changeset
797 </test>
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diff changeset
798 <test expect_num_outputs="1">
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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799 <!-- 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
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diff changeset
800 <param name="type" value="paired"/>
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diff changeset
801 <param name="paired_options_selector" value="no"/>
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diff changeset
802 <param name="unaligned_file" value="false"/>
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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diff changeset
803 <param name="analysis_type_selector" value="simple"/>
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diff changeset
804 <param name="source" value="history" />
cd8b7d755af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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diff changeset
805 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
806 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
807 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
808 <param name="sam_options_selector" value="yes" />
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diff changeset
809 <param name="sam_options|sam_opt" value="true" />
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810 <output name="output" ftype="sam">
31
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diff changeset
811 <metadata name="sort_order" value="unsorted"/>
24
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diff changeset
812 <assert_contents>
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813 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
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814 </assert_contents>
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diff changeset
815 </output>
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816 </test>
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817 </tests>
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818 <help><![CDATA[
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819 **Bowtie2 Overview**
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820
2
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821 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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822 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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823
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824 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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825 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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826 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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827
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828 -----
0
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829
2
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830 **Selecting reference genomes for Bowtie2**
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831
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832 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
0
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833
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834 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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835 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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836
2
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837 If your genome of interest is not listed here you have two choices:
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838
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839 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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840 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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841
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842 ------
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843
2
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844 .. class:: infomark
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diff changeset
845
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846 **Bowtie2 options**
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847
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848 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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849
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850 -----
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851
0
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852 **Inputs**
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853
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diff changeset
854 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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855
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856 ------
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857
2
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858 **Input options**::
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859
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860 --interleaved
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861 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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862
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863 -s/--skip <int>
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864 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
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865
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866 -u/--qupto <int>
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867 Align the first `<int>` reads or read pairs from the input (after the
2
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868 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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869
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870 -5/--trim5 <int>
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871 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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872
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873 -3/--trim3 <int>
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874 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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875
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diff changeset
876 --phred33
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877 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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878 also called the "Phred+33" encoding, which is used by the very latest Illumina
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879 pipelines.
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880
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diff changeset
881 --phred64
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882 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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883 also called the "Phred+64" encoding.
0
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884
2
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885 --solexa-quals
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886 Convert input qualities from Solexa Phred quality (which can be negative) to
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887 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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888 Pipeline versions (prior to 1.3). Default: off.
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889
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890 --int-quals
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891 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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892 Integers are treated as being on the Phred quality scale unless
2
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893 `--solexa-quals` is also specified. Default: off.
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894
2
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895 ------
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896
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897 **Presets in `--end-to-end` mode**::
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898
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899 --very-fast
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900 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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901
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902 --fast
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diff changeset
903 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
11
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parents: 10
diff changeset
904
2
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905 --sensitive
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diff changeset
906 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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parents: 1
diff changeset
907
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parents: 1
diff changeset
908 --very-sensitive
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diff changeset
909 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
910
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
911 ------
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
912
2
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diff changeset
913 **Presets options in `--local` mode**::
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
914
2
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diff changeset
915 --very-fast-local
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diff changeset
916 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
917
2
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diff changeset
918 --fast-local
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parents: 1
diff changeset
919 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
920
2
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diff changeset
921 --sensitive-local
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parents: 1
diff changeset
922 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
923
2
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parents: 1
diff changeset
924 --very-sensitive-local
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parents: 1
diff changeset
925 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
926
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
927 ------
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
928
2
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diff changeset
929 **Alignment options**::
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parents: 1
diff changeset
930
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fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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parents: 10
diff changeset
931 -N <int>
5
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diff changeset
932 Sets the number of mismatches to allowed in a seed alignment during multiseed
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
933 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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diff changeset
934 (often much slower) but increases sensitivity. Default: 0.
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diff changeset
935
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fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
936 -L <int>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
937 Sets the length of the seed substrings to align during multiseed alignment.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
938 Smaller values make alignment slower but more sensitive. Default: the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
939 `--sensitive` preset is used by default, which sets `-L` to 22 in
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
940 `--end-to-end` mode and to 20 in `--local` mode.
2
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diff changeset
941
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diff changeset
942 -i <func>
2
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diff changeset
943 Sets a function governing the interval between seed substrings to use during
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
944 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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diff changeset
945 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
946
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diff changeset
947 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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parents: 1
diff changeset
948 Seed 1 fw: TAGCTACGCT
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parents: 1
diff changeset
949 Seed 1 rc: AGCGTAGCTA
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parents: 1
diff changeset
950 Seed 2 fw: CGCTCTACGC
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parents: 1
diff changeset
951 Seed 2 rc: GCGTAGAGCG
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parents: 1
diff changeset
952 Seed 3 fw: ACGCTATCAT
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diff changeset
953 Seed 3 rc: ATGATAGCGT
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diff changeset
954 Seed 4 fw: TCATGCATAA
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955 Seed 4 rc: TTATGCATGA
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diff changeset
956
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diff changeset
957 Since it's best to use longer intervals for longer reads, this parameter sets
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958 the interval as a function of the read length, rather than a single
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diff changeset
959 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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diff changeset
960 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
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diff changeset
961 If the function returns a result less than
2
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diff changeset
962 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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963 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
964 in `--local` mode.
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965
11
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diff changeset
966 --n-ceil <func>
2
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diff changeset
967 Sets a function governing the maximum number of ambiguous characters (usually
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diff changeset
968 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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diff changeset
969 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
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diff changeset
970 where x is the read length. Reads exceeding this ceiling are filtered out.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
971 Default: `L,0,0.15`.
2
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972
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diff changeset
973 --dpad <int>
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974 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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975 gaps. Default: 15.
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diff changeset
976
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diff changeset
977 --gbar <int>
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diff changeset
978 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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979 Default: 4.
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980
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981 --ignore-quals
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diff changeset
982 When calculating a mismatch penalty, always consider the quality value at the
11
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983 mismatched position to be the highest possible, regardless of the actual value.
2
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984 I.e. input is treated as though all quality values are high. This is also the
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985 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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986 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
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diff changeset
987
2
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988 --nofw/--norc
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989 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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990 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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991 not attempt to align unpaired reads against the reverse-complement (Crick)
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diff changeset
992 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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diff changeset
993 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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994 paired-end configurations corresponding to fragments from the reverse-complement
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diff changeset
995 (Crick) strand. Default: both strands enabled.
2
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diff changeset
996
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diff changeset
997 --no-1mm-upfront
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diff changeset
998 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
5
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diff changeset
999 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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1000 alignments can be found very quickly, and many short read alignments have exact or
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diff changeset
1001 near-exact end-to-end alignments. However, this can lead to unexpected
5
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diff changeset
1002 alignments when the user also sets options governing the multiseed heuristic,
2
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1003 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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1004 to the length of the read, the user will be surprised to find 1-mismatch alignments
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diff changeset
1005 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
5
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diff changeset
1006 alignments before using the multiseed heuristic, which leads to the expected
2
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diff changeset
1007 behavior when combined with options such as `-L` and `-N`. This comes at the
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1008 expense of speed.
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diff changeset
1009
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1010 --end-to-end
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1011 In this mode, Bowtie 2 requires that the entire read align from one end to the
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1012 other, without any trimming (or "soft clipping") of characters from either end.
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1013 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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1014 are less than or equal to 0, and the greatest possible alignment score is 0.
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1015 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
a03a7ee6cdff Imported from capsule None
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parents:
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1016
2
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1017 --local
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1018 In this mode, Bowtie 2 does not require that the entire read align from one end
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1019 to the other. Rather, some characters may be omitted ("soft clipped") from the
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1020 ends in order to achieve the greatest possible alignment score. The match bonus
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1021 `--ma` is used in this mode, and the best possible alignment score is equal to
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1022 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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1023 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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1024 the local version of the preset (`--very-fast-local`). This is mutually
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1025 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1026
2
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1027 -----
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1028
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1029 **Scoring options**::
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1030
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1031 --ma <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1032 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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1033 score for each position where a read character aligns to a reference character
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1034 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1035
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1036 --mp MX,MN
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1037 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1038 number less than or equal to `MX` and greater than or equal to `MN` is
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1039 subtracted from the alignment score for each position where a read character
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1040 aligns to a reference character, the characters do not match, and neither is an
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1041 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1042 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1043 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1044
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1045 --np <int>
2
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1046 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1047 ambiguous character such as `N`. Default: 1.
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1048
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1049 --rdg <int1>,<int2>
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1050 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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diff changeset
1051 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1052
11
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diff changeset
1053 --rfg <int1>,<int2>
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parents: 10
diff changeset
1054 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1055 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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diff changeset
1056 5, 3.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1057
11
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diff changeset
1058 --score-min <func>
2
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diff changeset
1059 Sets a function governing the minimum alignment score needed for an alignment to
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diff changeset
1060 be considered "valid" (i.e. good enough to report). This is a function of read
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diff changeset
1061 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
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parents: 2
diff changeset
1062 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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parents: 1
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1063 the default in `--local` mode is `G,20,8`.
11
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diff changeset
1064
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diff changeset
1065 -----
2
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diff changeset
1066
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diff changeset
1067 **Reporting options**::
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1068
11
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diff changeset
1069 -k <int>
2
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diff changeset
1070 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1071 When it finds a valid alignment, it continues looking for alignments that are
2a6cfe8997aa Uploaded from GH
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diff changeset
1072 nearly as good or better. The best alignment found is reported (randomly
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1073 selected from among best if tied). Information about the best alignments is
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1074 used to estimate mapping quality and to set SAM optional fields, such as
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diff changeset
1075 `AS:i` and `XS:i`.
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diff changeset
1076
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diff changeset
1077 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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diff changeset
1078 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1079 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
1080 finds `<int>`, whichever happens first. All alignments found are reported in
2
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diff changeset
1081 descending order by alignment score. The alignment score for a paired-end
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1082 alignment equals the sum of the alignment scores of the individual mates. Each
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diff changeset
1083 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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1084 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1085 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1086 `<int>` alignments reported are the best possible in terms of alignment score.
2
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diff changeset
1087 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
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1088
2
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1089 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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diff changeset
1090 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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diff changeset
1091
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diff changeset
1092 -a
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1093 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1094 is mutually exclusive with `-k`.
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diff changeset
1095
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1096 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
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diff changeset
1097 aligning reads to long, repetitive genomes this mode can be very, very slow.
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diff changeset
1098
2
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1099 -----
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1100
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1101 **Effort options**::
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1102
11
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diff changeset
1103 -D <int>
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diff changeset
1104 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1105 moves on, using the alignments found so far. A seed extension "fails" if it
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1106 does not yield a new best or a new second-best alignment. This limit is
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1107 automatically adjusted up when -k or -a are specified. Default: 15.
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1108
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diff changeset
1109 -R <int>
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diff changeset
1110 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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1111 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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1112 (same length, same number of mismatches allowed) at different offsets and
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1113 searches for more alignments. A read is considered to have repetitive seeds if
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1114 the total number of seed hits divided by the number of seeds that aligned at
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1115 least once is greater than 300. Default: 2.
11
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1116
2
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diff changeset
1117 -----
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1118
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1119 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1120
11
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diff changeset
1121 -I/--minins <int>
2
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1122 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1123 specified and a paired-end alignment consists of two 20-bp alignments in the
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1124 appropriate orientation with a 20-bp gap between them, that alignment is
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1125 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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parents: 1
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1126 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1127 `-I` constraint is applied with respect to the untrimmed mates.
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1128
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1129 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1130 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
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diff changeset
1131 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1132 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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diff changeset
1133 efficient.
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1134
11
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1135 Default: 0 (essentially imposing no minimum)
2
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1136
11
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diff changeset
1137 -X/--maxins <int>
2
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1138 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1139 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1140 proper orientation with a 60-bp gap between them, that alignment is considered
2a6cfe8997aa Uploaded from GH
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diff changeset
1141 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
1142 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1143 constraint is applied with respect to the untrimmed mates, not the trimmed
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1144 mates.
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diff changeset
1145
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1146 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1147 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
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diff changeset
1148 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1149 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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1150 efficient.
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1151
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1152 Default: 500.
0
a03a7ee6cdff Imported from capsule None
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1153
2
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1154 --fr/--rf/--ff
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1155 The upstream/downstream mate orientations for a valid paired-end alignment
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1156 against the forward reference strand. E.g., if `--fr` is specified and there is
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diff changeset
1157 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1158 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1159 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1160 complement of mate 1 and all other constraints are met, that too is valid.
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1161 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1162 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1163 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1164 for Illumina's Paired-end Sequencing Assay).
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1165
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1166 --no-mixed
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1167 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1168 a pair, it then tries to find alignments for the individual mates. This option
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1169 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
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1170
2
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1171 --no-discordant
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1172 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1173 concordant alignments. A discordant alignment is an alignment where both mates
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1174 align uniquely, but that does not satisfy the paired-end constraints
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1175 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1176
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1177 --dovetail
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1178 If the mates "dovetail", that is if one mate alignment extends past the
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1179 beginning of the other such that the wrong mate begins upstream, consider that
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1180 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1181
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1182 --no-contain
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1183 If one mate alignment contains the other, consider that to be non-concordant.
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1184 Default: a mate can contain the other in a concordant alignment.
2
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1185
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1186 --no-overlap
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1187 If one mate alignment overlaps the other at all, consider that to be
5
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diff changeset
1188 non-concordant. Default: mates can overlap in a concordant alignment.
11
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1189
0
a03a7ee6cdff Imported from capsule None
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1190 ------
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1191
2
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1192 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
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1193
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diff changeset
1194 --rg-id <text>
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1195 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1196 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1197 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1198 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1199
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diff changeset
1200 --rg <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1201 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1202 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
1203 must also be specified. This is because the `ID` tag is required by the SAM
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
1204 Specification. Specify `--rg` multiple times to set multiple fields. See the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
1205 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1206
2
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parents: 1
diff changeset
1207 --omit-sec-seq
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parents: 1
diff changeset
1208 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
2a6cfe8997aa Uploaded from GH
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parents: 1
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1209 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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parents: 1
diff changeset
1210 in those fields instead.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1211
2
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parents: 1
diff changeset
1212 -----
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1213
2
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1214 **Other options**::
0
a03a7ee6cdff Imported from capsule None
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1215
2
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parents: 1
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1216 --reorder
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1217 Guarantees that output SAM records are printed in an order corresponding to the
2a6cfe8997aa Uploaded from GH
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parents: 1
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1218 order of the reads in the original input file, even when `-p` is set greater
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1219 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1220 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
2a6cfe8997aa Uploaded from GH
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1221 not specified. Has no effect if `-p` is set to 1, since output order will
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1222 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1223
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1224 --seed <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1225 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1226
2
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1227 --non-deterministic
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1228 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1229 seeds the generator with a number derived from (a) the read name, (b) the
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1230 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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diff changeset
1231 option. This means that if two reads are identical (same name, same
2a6cfe8997aa Uploaded from GH
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1232 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1233 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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diff changeset
1234 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1235 current time. This means that Bowtie 2 will not necessarily report the same
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diff changeset
1236 alignment for two identical reads. This is counter-intuitive for some users,
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1237 but might be more appropriate in situations where the input consists of many
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diff changeset
1238 identical reads.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1239
15
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1240 -----
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1241
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1242
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1243 **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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1244
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1245 Paired end datasets can be represented as two individual datasets:
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diff changeset
1246
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diff changeset
1247 First dataset::
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diff changeset
1248
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1249 @1/1
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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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1251 +
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diff changeset
1252 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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1253 @2/1
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diff changeset
1254 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1255 +
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1256 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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diff changeset
1257
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diff changeset
1258 Second dataset::
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diff changeset
1259
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diff changeset
1260 @1/2
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diff changeset
1261 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1262 +
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diff changeset
1263 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1264 @2/2
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diff changeset
1265 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1266 +
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1267 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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1268
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diff changeset
1269 Or a single *interleaved* dataset::
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1270
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1271 @1/1
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1272 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1273 +
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diff changeset
1274 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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diff changeset
1275 @1/2
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diff changeset
1276 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1277 +
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1278 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1279 @2/1
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diff changeset
1280 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1281 +
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1282 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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1283 @2/2
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1284 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1285 +
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1286 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1287 ]]></help>
2
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1288 <citations>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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parents: 16
diff changeset
1289 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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parents: 16
diff changeset
1290 <citation type="doi">10.1038/nmeth.1923</citation>
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diff changeset
1291 </citations>
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1292 </tool>