Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 22:c3dd1aeb7d07 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
author iuc
date Thu, 12 Apr 2018 17:42:40 -0400
parents 3ba8d4563129
children 17062a0decb7
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c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.2" profile="18.01">
2
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2 <description>- map reads against reference genome</description>
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42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
5
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.3.4">bowtie2</requirement>
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8 <requirement type="package" version="1.8">samtools</requirement>
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9 </requirements>
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96d2e31a3938 Imported from capsule None
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10 <version_command>bowtie2 --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## Use pipefail if available to quit with first non-zero exit code
3ba8d4563129 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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13 set -o | grep -q pipefail && set -o pipefail;
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14 ## prepare bowtie2 index
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15 #set index_path = ''
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16 #if str($reference_genome.source) == "history":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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18 ln -s -f '$reference_genome.own_file' genome.fa &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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19 #set index_path = 'genome'
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20 #else:
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21 #set index_path = $reference_genome.index.fields.path
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22 #end if
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24 ## Link in the input files, so bowtie2 can tell their type
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26 #set compressed="False"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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27 #set reads_are_fastq = True
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28 #if str($library.type) == 'paired':
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29 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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30 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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31 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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32 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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33 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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34 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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35 #else if $library.input_1.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #set reads_are_fastq = False
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37 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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38 #else:
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39 #set read1 = "input_f.fastq"
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40 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 ln -f -s '${library.input_1}' ${read1} &&
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42
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43 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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44 #set read2 = "input_r.fastq.gz"
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45 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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46 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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47 #set read2 = "input_r.fastq.bz2"
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48 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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49 #else if $library.input_2.is_of_type('fasta'):
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50 #set read2 = "input_r.fasta"
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51 #else:
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52 #set read2 = "input_r.fastq"
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53 #end if
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54 ln -f -s '${library.input_2}' ${read2} &&
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55 #else if str($library.type) == 'paired_collection':
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56 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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57 #set read1 = "input_f.fastq.gz"
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58 #set compressed = "GZ"
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59 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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60 #set read1 = "input_f.fastq.bz2"
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61 #set compressed = "BZ2"
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62 #else if $library.input_1.forward.is_of_type('fasta'):
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63 #set reads_are_fastq = False
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64 #set read1 = "input_f.fasta"
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65 #else:
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66 #set read1 = "input_f.fastq"
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67 #end if
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68 ln -s '${library.input_1.forward}' ${read1} &&
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69
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70 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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71 #set read2 = "input_r.fastq.gz"
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72 #set compressed = "GZ"
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73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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74 #set read2 = "input_r.fastq.bz2"
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75 #set compressed = "BZ2"
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76 #else if $library.input_1.reverse.is_of_type("fasta"):
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77 #set read2 = "input_r.fasta"
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78 #else:
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79 #set read2 = "input_r.fastq"
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80 #end if
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81 ln -s '${library.input_1.reverse}' ${read2} &&
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82
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83 #else if str($library.type) == 'paired_interleaved':
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84 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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85 #set read1 = "input_il.fastq.gz"
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86 #set compressed = "GZ"
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iuc
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diff changeset
87 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
88 #set read1 = "input_il.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
89 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
91 #set reads_are_fastq = False
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iuc
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diff changeset
92 #set read1 = "input_il.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
94 #set read1 = "input_il.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
95 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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96 ln -s '${library.input_1}' ${read1} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
97 #else:
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iuc
parents: 17
diff changeset
98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
99 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
100 #set compressed = "GZ"
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iuc
parents: 17
diff changeset
101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
102 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
103 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
104 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
107 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
108 #set read1 = "input_f.fastq"
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iuc
parents: 17
diff changeset
109 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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110 ln -s '${library.input_1}' ${read1} &&
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iuc
parents: 17
diff changeset
111 #end if
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iuc
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diff changeset
112
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113 ## execute bowtie2
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114
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115 bowtie2
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116
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117 ## number of threads
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118 -p \${GALAXY_SLOTS:-4}
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119
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120 ## index file path
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121 -x '$index_path'
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122
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diff changeset
123 ## Input reads are fasta?
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124 #if not reads_are_fastq:
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diff changeset
125 -f
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diff changeset
126 #end if
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127
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128 ## Input reads
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129 #if str( $library.type ) == "single":
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130 -U '${read1}'
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iuc
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diff changeset
131 #if str( $library.unaligned_file ) == "true":
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iuc
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132 #if $compressed == "GZ":
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iuc
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diff changeset
133 --un-gz '${output_unaligned_reads_l}'
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iuc
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diff changeset
134 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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135 --un-bz2 '${output_unaligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
136 #else:
18
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137 --un '${output_unaligned_reads_l}'
14
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devteam
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diff changeset
138 #end if
18
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diff changeset
139 #end if
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iuc
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140 #if str( $library.aligned_file ) == "true":
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iuc
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141 #if $compressed == "GZ":
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iuc
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diff changeset
142 --al-gz '${output_aligned_reads_l}'
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iuc
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diff changeset
143 #else if $compressed == "BZ2":
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iuc
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diff changeset
144 --al-bz2 '${output_aligned_reads_l}'
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145 #else:
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146 --al '${output_aligned_reads_l}'
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
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diff changeset
147 #end if
18
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148 #end if
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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149
18
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150 #elif str( $library.type ) == "paired_interleaved":
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151 --interleaved '${read1}'
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152 #if str( $library.unaligned_file ) == "true":
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iuc
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153 #if $compressed == "GZ":
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diff changeset
154 --un-gz '${output_unaligned_reads_l}'
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iuc
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155 #else if $compressed == "BZ2":
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iuc
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diff changeset
156 --un-bz2 '${output_unaligned_reads_l}'
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iuc
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diff changeset
157 #else:
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iuc
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diff changeset
158 --un '${output_unaligned_reads_l}'
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iuc
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diff changeset
159 #end if
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diff changeset
160 #end if
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diff changeset
161 #if str( $library.aligned_file ) == "true":
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iuc
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162 #if $compressed == "GZ":
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iuc
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diff changeset
163 --al-gz '${output_aligned_reads_l}'
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iuc
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diff changeset
164 #else if $compressed == "BZ2":
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diff changeset
165 --al-bz2 '${output_aligned_reads_l}'
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iuc
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diff changeset
166 #else:
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iuc
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diff changeset
167 --al '${output_aligned_reads_l}'
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iuc
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diff changeset
168 #end if
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iuc
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diff changeset
169 #end if
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diff changeset
170 #else:
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171 -1 '${read1}'
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iuc
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diff changeset
172 -2 '${read2}'
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iuc
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diff changeset
173 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
174 #if $compressed == "GZ":
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iuc
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diff changeset
175 --un-conc-gz '${output_unaligned_reads_l}'
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iuc
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diff changeset
176 #else if $compressed == "BZ2":
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iuc
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diff changeset
177 --un-conc-bz2 '${output_unaligned_reads_l}'
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178 #else:
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179 --un-conc '${output_unaligned_reads_l}'
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180 #end if
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181 #end if
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182 #if str( $library.aligned_file ) == "true":
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183 #if $compressed == "GZ":
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184 --al-conc-gz '${output_aligned_reads_l}'
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185 #else if $compressed == "BZ2":
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186 --al-conc-bz2 '${output_aligned_reads_l}'
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187 #else:
18
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188 --al-conc '${output_aligned_reads_l}'
0
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189 #end if
18
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190 #end if
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191 #if str( $library.paired_options.paired_options_selector ) == "yes":
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192 -I ${library.paired_options.I}
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193 -X ${library.paired_options.X}
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194 ${library.paired_options.fr_rf_ff}
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195 ${library.paired_options.no_mixed}
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196 ${library.paired_options.no_discordant}
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197 ${library.paired_options.dovetail}
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198 ${library.paired_options.no_contain}
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199 ${library.paired_options.no_overlap}
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200 #end if
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201 #end if
7
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202
18
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203 ## Read group information.
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204 @define_read_group_helpers@
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205 #if str( $library.type ) == "single":
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206 #set $rg_auto_name = $read_group_name_default($library.input_1)
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207 #elif str( $library.type ) == "paired":
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208 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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209 #else
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210 #set $rg_auto_name = $read_group_name_default($library.input_1)
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211 #end if
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212 @set_use_rg_var@
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213 @set_read_group_vars@
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214 #if $use_rg
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215 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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216 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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217 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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218 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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219 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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220 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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221 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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222 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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223 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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224 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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225 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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226 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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227 #end if
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228
18
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229 ## Analysis type
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230 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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231 $analysis_type.presets
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232 #elif str( $analysis_type.analysis_type_selector ) == "full":
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233 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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234 --skip ${analysis_type.input_options.skip}
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235 --qupto ${analysis_type.input_options.qupto}
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236 --trim5 ${analysis_type.input_options.trim5}
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237 --trim3 ${analysis_type.input_options.trim3}
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238 ${analysis_type.input_options.qv_encoding}
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239 ${analysis_type.input_options.solexa_quals}
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240 ${analysis_type.input_options.int_quals}
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241 #end if
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242
18
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243 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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244 -N ${analysis_type.alignment_options.N}
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245 -L ${analysis_type.alignment_options.L}
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246 -i '${analysis_type.alignment_options.i}'
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247 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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248 --dpad ${analysis_type.alignment_options.dpad}
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249 --gbar ${analysis_type.alignment_options.gbar}
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250 ${analysis_type.alignment_options.ignore_quals}
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251 ${analysis_type.alignment_options.nofw}
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252 ${analysis_type.alignment_options.norc}
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253 ${analysis_type.alignment_options.no_1mm_upfront}
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254 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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255 --end-to-end
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256 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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257 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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258 --local
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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260 #end if
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261 #end if
7
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262
18
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263 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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264 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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265 --ma ${analysis_type.scoring_options.ma}
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266 #end if
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267 --mp '${analysis_type.scoring_options.mp}'
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268 --np ${analysis_type.scoring_options.np}
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269 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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270 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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271 #end if
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272
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273 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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274 -k ${analysis_type.reporting_options.k}
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275 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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276 -a
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277 #end if
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278
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279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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280 -D ${analysis_type.effort_options.D}
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281 -R ${analysis_type.effort_options.R}
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282 #end if
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283 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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284 ${analysis_type.other_options.reorder}
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285 ${analysis_type.other_options.non_deterministic}
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286 --seed ${analysis_type.other_options.seed}
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287 #end if
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288
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289 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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290 ${analysis_type.cline}
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291 #end if
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292
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293 #if str( $sam_options.sam_options_selector ) == "yes":
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294 ${sam_options.no_unal}
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295 ${sam_options.omit_sec_seq}
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296 ${sam_options.sam_no_qname_trunc}
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297 ${sam_options.xeq}
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298 ${sam_options.soft_clipped_unmapped_tlen}
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299 ${sam_options.reorder}
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300 #end if
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301
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302 ## mapping stats (i.e. stderr from bowtie2)
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303 #if $save_mapping_stats
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304 2> '$mapping_stats'
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305 #end if
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306
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307 ## output file
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308 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
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309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
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310 #else if $sam_options.reorder:
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311 | samtools view -bS - -o '$output'
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312 #else:
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313 > '$output_sam'
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314 #end if
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315
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316 ## rename unaligned sequence files
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317 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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318 #from os.path import splitext
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319 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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320 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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321 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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322 #end if
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323 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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324 #from os.path import splitext
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325 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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326 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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327 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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328 #end if
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329
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330 ]]></command>
0
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331 <inputs>
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332 <!-- single/paired -->
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333 <conditional name="library">
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334 <param name="type" type="select" label="Is this single or paired library">
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335 <option value="single">Single-end</option>
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336 <option value="paired">Paired-end</option>
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337 <option value="paired_collection">Paired-end Dataset Collection</option>
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338 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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339 </param>
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340
0
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341 <when value="single">
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342 <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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343 <expand macro="align_unalign" />
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344 </when>
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345 <when value="paired">
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346 <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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347 <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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348 <expand macro="align_unalign" />
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349 <expand macro="paired_end_options" />
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350 </when>
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351 <when value="paired_collection">
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352 <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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353 <expand macro="align_unalign" />
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354 <expand macro="paired_end_options" />
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355 </when>
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356 <when value="paired_interleaved">
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357 <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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358 <expand macro="align_unalign" />
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359 <expand macro="paired_end_options" />
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360 </when>
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361 </conditional>
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362 <!-- reference genome -->
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363 <conditional name="reference_genome">
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364 <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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365 <option value="indexed">Use a built-in genome index</option>
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366 <option value="history">Use a genome from the history and build index</option>
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367 </param>
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368 <when value="indexed">
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369 <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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370 <options from_data_table="bowtie2_indexes">
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371 <filter type="sort_by" column="2"/>
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372 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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373 </options>
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374 </param>
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375 </when>
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376 <when value="history">
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377 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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378 </when>
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379 </conditional>
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380 <!-- read group settings -->
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381 <expand macro="read_group_conditional" />
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382 <conditional name="analysis_type">
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383 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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384 <option value="simple">1: Default setting only</option>
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385 <option value="full">2: Full parameter list</option>
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386 </param>
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387 <when value="simple">
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388 <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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389 <option value="no_presets" selected="True">No, just use defaults</option>
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390 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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391 <option value="--fast">Fast end-to-end (--fast)</option>
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392 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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393 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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394 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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395 <option value="--fast-local">Fast local (--fast-local)</option>
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396 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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397 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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398 </param>
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399 </when>
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400 <when value="full">
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401 <conditional name="input_options">
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402 <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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403 <option value="yes">Yes</option>
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404 <option value="no" selected="true">No</option>
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405 </param>
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406 <when value="yes">
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407 <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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408 <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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409 <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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410 <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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411 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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412 <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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413 <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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414 </param>
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415 <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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416 <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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417 </when>
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418 <when value="no">
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419 <!-- do nothing -->
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420 </when>
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421 </conditional>
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422 <conditional name="alignment_options">
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423 <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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424 <option value="yes">Yes</option>
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425 <option value="no" selected="true">No</option>
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426 </param>
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427 <when value="yes">
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428 <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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429 <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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430 <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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431 <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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432 <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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433 <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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434 <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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435 <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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436 <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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437 <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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438 <conditional name="align_mode">
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439 <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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440 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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441 <option value="local">Local (--local)</option>
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442 </param>
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443 <when value="end-to-end">
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444 <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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445 </when>
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446 <when value="local">
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447 <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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448 </when>
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449 </conditional>
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450 </when>
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451 <when value="no">
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452 <!-- do nothing -->
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453 </when>
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454 </conditional>
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455 <conditional name="scoring_options">
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456 <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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457 <option value="yes">Yes</option>
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458 <option value="no" selected="true">No</option>
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459 </param>
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460 <when value="yes">
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461 <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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462 <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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463 <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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464 <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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465 <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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466 <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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467 <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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468 </when>
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469 <when value="no">
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470 <!-- do nothing -->
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471 </when>
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472 </conditional>
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473 <conditional name="reporting_options">
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474 <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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475 <option value="no" selected="true">No, do not set</option>
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476 <option value="k">Set -k option and enter -k value</option>
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477 <option value="a">Set -a option</option>
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478 </param>
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479 <when value="no">
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480 <!-- do nothing -->
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481 </when>
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482 <when value="k">
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483 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
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484 </when>
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485 <when value="a">
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486 <!-- do nothing here; set -a flag on the command line-->
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487 </when>
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parents: 0
diff changeset
488 </conditional>
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parents: 0
diff changeset
489 <conditional name="effort_options">
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parents: 0
diff changeset
490 <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">
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
491 <option value="yes">Yes</option>
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parents: 0
diff changeset
492 <option value="no" selected="true">No</option>
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parents: 0
diff changeset
493 </param>
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parents: 0
diff changeset
494 <when value="yes">
3
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parents: 2
diff changeset
495 <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
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
496 <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"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
497 </when>
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devteam
parents: 0
diff changeset
498 <when value="no">
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parents: 0
diff changeset
499 <!-- do nothing -->
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
500 </when>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
501 </conditional>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
502 <conditional name="other_options">
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
503 <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">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
504 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
505 <option value="no" selected="true">No</option>
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parents: 0
diff changeset
506 </param>
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parents: 0
diff changeset
507 <when value="yes">
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
508 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file. If selected output file will not be coordinate sorted." help="--reorder; Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
509 <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"/>
3
ceb6467e276c Uploaded
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parents: 2
diff changeset
510 <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
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
511 </when>
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parents: 0
diff changeset
512 <when value="no">
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parents: 0
diff changeset
513 <!-- do nothing -->
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parents: 0
diff changeset
514 </when>
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parents: 0
diff changeset
515 </conditional>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
516 </when>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
517 </conditional>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
518 <conditional name="sam_options">
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
519 <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">
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
520 <option value="yes">Yes</option>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
521 <option value="no" selected="true">No</option>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
522 </param>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
523 <when value="yes">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
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524 <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."/>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
525 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
526 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
527 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
528 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
529 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
530 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
531 label="Reorder output to reflect order of the input file"
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
532 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
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
533 </when>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
534 <when value="no"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
535 </conditional>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
537 </inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
538 <!-- define outputs -->
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
539 <outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
540 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
541 <filter>library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
542 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
543 <conditional name="library.type">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
544 <when value="single">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
545 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
546 <option type="from_param" name="library.input_1" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
547 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
548 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
549 <when value="paired">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
550 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
551 <option type="from_param" name="library.input_1" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
552 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
553 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
554 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
555 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
556 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
557 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
558 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
559 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
560 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
561 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
562 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
563 <filter>library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
564 <actions>
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parents: 8
diff changeset
565 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
566 <when value="single">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
567 <action type="format">
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diff changeset
568 <option type="from_param" name="library.input_1" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
569 </action>
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parents: 8
diff changeset
570 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
571 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
572 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
573 <option type="from_param" name="library.input_1" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
574 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
575 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
576 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
577 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
578 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
579 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
580 </when>
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parents: 8
diff changeset
581 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
582 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
583 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
584 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
585 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
586 <actions>
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parents: 8
diff changeset
587 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
588 <when value="paired">
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parents: 8
diff changeset
589 <action type="format">
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devteam
parents: 8
diff changeset
590 <option type="from_param" name="library.input_2" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
591 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
592 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
593 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
594 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
595 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
596 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
597 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
598 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
599 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
600 </data>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
601 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
602 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
603 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
604 <conditional name="library.type">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
605 <when value="paired">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
606 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
607 <option type="from_param" name="library.input_2" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
608 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
609 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
610 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
611 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
612 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
613 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
614 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
615 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
616 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
617 </data>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
618 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
619 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
620 <change_format>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
621 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
622 </change_format>
7
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devteam
parents: 6
diff changeset
623 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
624 <conditional name="reference_genome.source">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
625 <when value="indexed">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
626 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
628 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
629 <filter type="param_value" ref="reference_genome.index" column="0"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
630 </option>
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devteam
parents: 6
diff changeset
631 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
632 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
633 <when value="history">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
634 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
636 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
637 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
638 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
639 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
640 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
641 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
642 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
643 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
644 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
645 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
646 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
647 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
648 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
649 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
650 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
651 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
652 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
653 <when value="history">
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
654 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
655 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
656 </action>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
657 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
658 </conditional>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
659 </actions>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
660 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
661 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
662 <filter>save_mapping_stats is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
663 </data>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
664 </outputs>
96d2e31a3938 Imported from capsule None
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665 <tests>
96d2e31a3938 Imported from capsule None
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666 <test>
17
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parents: 16
diff changeset
667 <!-- test on paired-end datasets -->
2
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devteam
parents: 0
diff changeset
668 <param name="type" value="paired"/>
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parents: 0
diff changeset
669 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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670 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
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671 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
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672 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
673 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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parents: 0
diff changeset
674 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
675 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 0
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676 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
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677 </test>
5
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parents: 4
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678 <test>
17
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iuc
parents: 16
diff changeset
679 <!-- test on paired collection -->
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iuc
parents: 16
diff changeset
680 <param name="type" value="paired_collection"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
681 <param name="paired_options_selector" value="no"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 <param name="unaligned_file" value="false"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
683 <param name="analysis_type_selector" value="simple"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
684 <param name="source" value="history" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
685 <param name="input_1">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <collection type="paired">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
688 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
689 </collection>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
690 </param>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
691 <param name="own_file" value="bowtie2-ref.fasta" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
692 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
693 </test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
694 <test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
695 <!-- test on paired-end datasets with read group info -->
5
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devteam
parents: 4
diff changeset
696 <param name="type" value="paired"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
697 <param name="paired_options_selector" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
698 <param name="unaligned_file" value="false"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
699 <param name="analysis_type_selector" value="simple"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
700 <param name="rg_selector" value="set"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
701 <param name="ID" value="rg1"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
702 <param name="PL" value="CAPILLARY"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
703 <param name="source" value="history" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
704 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
705 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
706 <param name="own_file" value="bowtie2-ref.fasta" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
707 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
708 </test>
10
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devteam
parents: 8
diff changeset
709 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
710 <!-- test on paired-end datasets with stats output -->
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
711 <param name="type" value="paired"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
712 <param name="paired_options_selector" value="no"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
713 <param name="unaligned_file" value="false"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
714 <param name="analysis_type_selector" value="simple"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
715 <param name="source" value="history" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
716 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
717 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
718 <param name="own_file" value="bowtie2-ref.fasta" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
719 <param name="save_mapping_stats" value="true" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
720 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
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iuc
parents: 14
diff changeset
721 <output name="mapping_stats">
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 <assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 <has_text text="of these" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
724 </assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
725 </output>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 </test>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
728 <!-- test on interleaved dataset -->
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
729 <param name="type" value="paired_interleaved"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 <!-- <param name="paired_options_selector" value="no"/> -->
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
731 <param name="unaligned_file" value="false"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
732 <param name="analysis_type_selector" value="simple"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
733 <param name="rg_selector" value="set"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
734 <param name="ID" value="rg1"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
735 <param name="PL" value="CAPILLARY"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
736 <param name="source" value="history" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
737 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
738 <param name="own_file" value="bowtie2-ref.fasta" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
739 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
740 </test>
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
741 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
742 <!-- test on fastqsanger.gz paired-end datasets -->
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
743 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
746 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
747 <param name="source" value="history" />
937aa69e715f 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_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
749 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
750 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
751 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
752 </test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
754 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
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parents: 13
diff changeset
755 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
756 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
757 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
758 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
759 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
760 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f 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_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
762 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
763 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
764 </test>
16
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iuc
parents: 15
diff changeset
765 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
766 <!-- test on fasta paired-end datasets -->
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
767 <param name="type" value="paired"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
768 <param name="paired_options_selector" value="no"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
769 <param name="unaligned_file" value="false"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
770 <param name="analysis_type_selector" value="simple"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
771 <param name="source" value="history" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
772 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
773 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
774 <param name="own_file" value="bowtie2-ref.fasta" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
775 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
776 </test>
22
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iuc
parents: 21
diff changeset
777 <test>
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parents: 21
diff changeset
778 <!-- test on fasta paired-end datasets with bam_native as output -->
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
779 <param name="type" value="paired"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
780 <param name="paired_options_selector" value="no"/>
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diff changeset
781 <param name="unaligned_file" value="false"/>
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diff changeset
782 <param name="analysis_type_selector" value="simple"/>
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diff changeset
783 <param name="source" value="history" />
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diff changeset
784 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
785 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
786 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
787 <param name="sam_options_selector" value="yes" />
c3dd1aeb7d07 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="reorder" value="true" />
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diff changeset
789 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
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790 </test>
0
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791 </tests>
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792 <help><![CDATA[
0
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793 **Bowtie2 Overview**
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794
2
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795 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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796 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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797
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798 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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799 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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800 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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801
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802 -----
0
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803
2
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804 **Selecting reference genomes for Bowtie2**
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805
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806 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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807
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diff changeset
808 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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809 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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810
2
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811 If your genome of interest is not listed here you have two choices:
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812
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813 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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814 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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815
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816 ------
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817
2
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818 .. class:: infomark
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819
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820 **Bowtie2 options**
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821
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822 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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823
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824 -----
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825
0
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826 **Inputs**
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827
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828 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).
0
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829
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830 ------
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831
2
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832 **Input options**::
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833
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834 --interleaved
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835 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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836
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837 -s/--skip <int>
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838 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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839
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840 -u/--qupto <int>
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841 Align the first `<int>` reads or read pairs from the input (after the
2
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842 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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843
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844 -5/--trim5 <int>
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845 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
0
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846
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847 -3/--trim3 <int>
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848 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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849
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850 --phred33
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851 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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852 also called the "Phred+33" encoding, which is used by the very latest Illumina
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853 pipelines.
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854
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855 --phred64
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856 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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857 also called the "Phred+64" encoding.
0
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858
2
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859 --solexa-quals
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860 Convert input qualities from Solexa Phred quality (which can be negative) to
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861 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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862 Pipeline versions (prior to 1.3). Default: off.
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863
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864 --int-quals
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865 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`....
3
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866 Integers are treated as being on the Phred quality scale unless
2
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867 `--solexa-quals` is also specified. Default: off.
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868
2
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869 ------
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870
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871 **Presets in `--end-to-end` mode**::
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872
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873 --very-fast
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874 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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875
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876 --fast
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877 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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878
2
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879 --sensitive
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880 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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881
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882 --very-sensitive
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883 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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884
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885 ------
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886
2
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887 **Presets options in `--local` mode**::
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888
2
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889 --very-fast-local
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890 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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891
2
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892 --fast-local
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893 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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894
2
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895 --sensitive-local
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896 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
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897
2
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898 --very-sensitive-local
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899 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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900
0
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901 ------
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902
2
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903 **Alignment options**::
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904
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905 -N <int>
3
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906 Sets the number of mismatches to allowed in a seed alignment during multiseed
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907 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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908 (often much slower) but increases sensitivity. Default: 0.
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909
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910 -L <int>
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911 Sets the length of the seed substrings to align during multiseed alignment.
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912 Smaller values make alignment slower but more sensitive. Default: the
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913 `--sensitive` preset is used by default, which sets `-L` to 22 in
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914 `--end-to-end` mode and to 20 in `--local` mode.
2
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915
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916 -i <func>
2
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917 Sets a function governing the interval between seed substrings to use during
3
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918 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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919 length is 10, and the seed interval is 6, the seeds extracted will be:
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920
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921 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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922 Seed 1 fw: TAGCTACGCT
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923 Seed 1 rc: AGCGTAGCTA
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924 Seed 2 fw: CGCTCTACGC
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925 Seed 2 rc: GCGTAGAGCG
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926 Seed 3 fw: ACGCTATCAT
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927 Seed 3 rc: ATGATAGCGT
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928 Seed 4 fw: TCATGCATAA
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929 Seed 4 rc: TTATGCATGA
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930
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diff changeset
931 Since it's best to use longer intervals for longer reads, this parameter sets
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diff changeset
932 the interval as a function of the read length, rather than a single
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diff changeset
933 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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diff changeset
934 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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parents: 2
diff changeset
935 If the function returns a result less than
2
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parents: 0
diff changeset
936 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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parents: 0
diff changeset
937 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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parents: 0
diff changeset
938 in `--local` mode.
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diff changeset
939
11
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parents: 10
diff changeset
940 --n-ceil <func>
2
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parents: 0
diff changeset
941 Sets a function governing the maximum number of ambiguous characters (usually
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parents: 0
diff changeset
942 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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parents: 0
diff changeset
943 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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parents: 2
diff changeset
944 where x is the read length. Reads exceeding this ceiling are filtered out.
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parents: 2
diff changeset
945 Default: `L,0,0.15`.
2
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parents: 0
diff changeset
946
11
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parents: 10
diff changeset
947 --dpad <int>
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diff changeset
948 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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diff changeset
949 gaps. Default: 15.
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parents: 0
diff changeset
950
11
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parents: 10
diff changeset
951 --gbar <int>
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diff changeset
952 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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953 Default: 4.
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954
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diff changeset
955 --ignore-quals
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diff changeset
956 When calculating a mismatch penalty, always consider the quality value at the
11
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diff changeset
957 mismatched position to be the highest possible, regardless of the actual value.
2
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958 I.e. input is treated as though all quality values are high. This is also the
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959 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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960 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
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961
2
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962 --nofw/--norc
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963 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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964 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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965 not attempt to align unpaired reads against the reverse-complement (Crick)
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diff changeset
966 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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967 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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968 paired-end configurations corresponding to fragments from the reverse-complement
11
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diff changeset
969 (Crick) strand. Default: both strands enabled.
2
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970
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971 --no-1mm-upfront
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972 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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973 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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974 alignments can be found very quickly, and many short read alignments have exact or
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975 near-exact end-to-end alignments. However, this can lead to unexpected
3
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976 alignments when the user also sets options governing the multiseed heuristic,
2
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977 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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978 to the length of the read, the user will be surprised to find 1-mismatch alignments
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979 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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980 alignments before using the multiseed heuristic, which leads to the expected
2
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981 behavior when combined with options such as `-L` and `-N`. This comes at the
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982 expense of speed.
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983
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984 --end-to-end
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985 In this mode, Bowtie 2 requires that the entire read align from one end to the
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986 other, without any trimming (or "soft clipping") of characters from either end.
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987 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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988 are less than or equal to 0, and the greatest possible alignment score is 0.
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989 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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990
2
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991 --local
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992 In this mode, Bowtie 2 does not require that the entire read align from one end
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993 to the other. Rather, some characters may be omitted ("soft clipped") from the
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994 ends in order to achieve the greatest possible alignment score. The match bonus
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995 `--ma` is used in this mode, and the best possible alignment score is equal to
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diff changeset
996 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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997 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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998 the local version of the preset (`--very-fast-local`). This is mutually
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diff changeset
999 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1000
2
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1001 -----
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1002
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diff changeset
1003 **Scoring options**::
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1004
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diff changeset
1005 --ma <int>
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diff changeset
1006 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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1007 score for each position where a read character aligns to a reference character
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1008 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1009
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1010 --mp MX,MN
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diff changeset
1011 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1012 number less than or equal to `MX` and greater than or equal to `MN` is
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1013 subtracted from the alignment score for each position where a read character
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1014 aligns to a reference character, the characters do not match, and neither is an
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diff changeset
1015 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1016 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1017 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1018
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diff changeset
1019 --np <int>
2
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diff changeset
1020 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1021 ambiguous character such as `N`. Default: 1.
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1022
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diff changeset
1023 --rdg <int1>,<int2>
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1024 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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diff changeset
1025 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1026
11
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diff changeset
1027 --rfg <int1>,<int2>
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1028 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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diff changeset
1029 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1030 5, 3.
0
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1031
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1032 --score-min <func>
2
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1033 Sets a function governing the minimum alignment score needed for an alignment to
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1034 be considered "valid" (i.e. good enough to report). This is a function of read
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1035 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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1036 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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1037 the default in `--local` mode is `G,20,8`.
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1038
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1039 -----
2
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1040
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diff changeset
1041 **Reporting options**::
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1042
11
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1043 -k <int>
2
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1044 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1045 When it finds a valid alignment, it continues looking for alignments that are
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1046 nearly as good or better. The best alignment found is reported (randomly
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1047 selected from among best if tied). Information about the best alignments is
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1048 used to estimate mapping quality and to set SAM optional fields, such as
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1049 `AS:i` and `XS:i`.
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1050
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1051 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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1052 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1053 search terminates when it can't find more distinct valid alignments, or when it
11
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1054 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1055 descending order by alignment score. The alignment score for a paired-end
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1056 alignment equals the sum of the alignment scores of the individual mates. Each
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1057 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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1058 (which equals 256) set in its FLAGS field. For reads that have more than
11
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1059 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
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1060 `<int>` alignments reported are the best possible in terms of alignment score.
2
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1061 `-k` is mutually exclusive with `-a`.
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1062
2
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1063 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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1064 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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1065
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1066 -a
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1067 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1068 is mutually exclusive with `-k`.
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1069
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1070 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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1071 aligning reads to long, repetitive genomes this mode can be very, very slow.
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1072
2
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diff changeset
1073 -----
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1074
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diff changeset
1075 **Effort options**::
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1076
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1077 -D <int>
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1078 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1079 moves on, using the alignments found so far. A seed extension "fails" if it
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diff changeset
1080 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
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diff changeset
1081 automatically adjusted up when -k or -a are specified. Default: 15.
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diff changeset
1082
11
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diff changeset
1083 -R <int>
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diff changeset
1084 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
c1ec08cb34f9 Uploaded
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diff changeset
1085 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
c1ec08cb34f9 Uploaded
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diff changeset
1086 (same length, same number of mismatches allowed) at different offsets and
c1ec08cb34f9 Uploaded
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diff changeset
1087 searches for more alignments. A read is considered to have repetitive seeds if
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1088 the total number of seed hits divided by the number of seeds that aligned at
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1089 least once is greater than 300. Default: 2.
11
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diff changeset
1090
2
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diff changeset
1091 -----
c1ec08cb34f9 Uploaded
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diff changeset
1092
c1ec08cb34f9 Uploaded
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diff changeset
1093 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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1094
11
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diff changeset
1095 -I/--minins <int>
2
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diff changeset
1096 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
c1ec08cb34f9 Uploaded
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1097 specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
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diff changeset
1098 appropriate orientation with a 20-bp gap between them, that alignment is
c1ec08cb34f9 Uploaded
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diff changeset
1099 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
c1ec08cb34f9 Uploaded
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1100 be valid in that case. If trimming options `-3` or `-5` are also used, the
c1ec08cb34f9 Uploaded
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diff changeset
1101 `-I` constraint is applied with respect to the untrimmed mates.
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diff changeset
1102
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diff changeset
1103 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1104 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1105 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1106 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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diff changeset
1107 efficient.
c1ec08cb34f9 Uploaded
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diff changeset
1108
11
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diff changeset
1109 Default: 0 (essentially imposing no minimum)
2
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diff changeset
1110
11
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diff changeset
1111 -X/--maxins <int>
2
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diff changeset
1112 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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diff changeset
1113 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1114 proper orientation with a 60-bp gap between them, that alignment is considered
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diff changeset
1115 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
1116 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1117 constraint is applied with respect to the untrimmed mates, not the trimmed
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1118 mates.
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1119
c1ec08cb34f9 Uploaded
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diff changeset
1120 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
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diff changeset
1121 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1122 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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diff changeset
1123 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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1124 efficient.
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diff changeset
1125
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1126 Default: 500.
0
96d2e31a3938 Imported from capsule None
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1127
2
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1128 --fr/--rf/--ff
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1129 The upstream/downstream mate orientations for a valid paired-end alignment
c1ec08cb34f9 Uploaded
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diff changeset
1130 against the forward reference strand. E.g., if `--fr` is specified and there is
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1131 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1132 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1133 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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diff changeset
1134 complement of mate 1 and all other constraints are met, that too is valid.
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1135 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1136 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1137 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1138 for Illumina's Paired-end Sequencing Assay).
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1139
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1140 --no-mixed
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1141 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1142 a pair, it then tries to find alignments for the individual mates. This option
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1143 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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1144
2
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1145 --no-discordant
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1146 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1147 concordant alignments. A discordant alignment is an alignment where both mates
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1148 align uniquely, but that does not satisfy the paired-end constraints
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1149 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1150
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1151 --dovetail
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1152 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
1153 beginning of the other such that the wrong mate begins upstream, consider that
3
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1154 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1155
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1156 --no-contain
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1157 If one mate alignment contains the other, consider that to be non-concordant.
3
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1158 Default: a mate can contain the other in a concordant alignment.
2
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1159
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1160 --no-overlap
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1161 If one mate alignment overlaps the other at all, consider that to be
3
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1162 non-concordant. Default: mates can overlap in a concordant alignment.
11
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1163
0
96d2e31a3938 Imported from capsule None
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1164 ------
96d2e31a3938 Imported from capsule None
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1165
2
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1166 **SAM options**::
0
96d2e31a3938 Imported from capsule None
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1167
11
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1168 --rg-id <text>
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diff changeset
1169 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1170 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1171 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1172 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
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1173
11
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1174 --rg <text>
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diff changeset
1175 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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diff changeset
1176 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
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1177 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1178 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1179 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
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1180
2
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1181 --omit-sec-seq
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1182 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
c1ec08cb34f9 Uploaded
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1183 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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diff changeset
1184 in those fields instead.
11
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diff changeset
1185
2
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1186 -----
0
96d2e31a3938 Imported from capsule None
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1187
2
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1188 **Other options**::
0
96d2e31a3938 Imported from capsule None
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1189
2
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1190 --reorder
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1191 Guarantees that output SAM records are printed in an order corresponding to the
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1192 order of the reads in the original input file, even when `-p` is set greater
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1193 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1194 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1195 not specified. Has no effect if `-p` is set to 1, since output order will
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1196 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
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1197
11
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1198 --seed <int>
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1199 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
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1200
2
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1201 --non-deterministic
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1202 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
c1ec08cb34f9 Uploaded
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1203 seeds the generator with a number derived from (a) the read name, (b) the
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1204 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1205 option. This means that if two reads are identical (same name, same
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1206 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1207 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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diff changeset
1208 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1209 current time. This means that Bowtie 2 will not necessarily report the same
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diff changeset
1210 alignment for two identical reads. This is counter-intuitive for some users,
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1211 but might be more appropriate in situations where the input consists of many
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1212 identical reads.
0
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1213
15
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1214 -----
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iuc
parents: 14
diff changeset
1215
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iuc
parents: 14
diff changeset
1216
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iuc
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diff changeset
1217 **Paired-end (and mate-pair) data in fastq format**
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iuc
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1218
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iuc
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diff changeset
1219 Paired end datasets can be represented as two individual datasets:
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iuc
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1220
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iuc
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diff changeset
1221 First dataset::
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iuc
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diff changeset
1222
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iuc
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diff changeset
1223 @1/1
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iuc
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diff changeset
1224 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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iuc
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diff changeset
1225 +
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iuc
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diff changeset
1226 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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diff changeset
1227 @2/1
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iuc
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diff changeset
1228 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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iuc
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1229 +
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diff changeset
1230 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1231
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1232 Second dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1233
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1234 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1235 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1236 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1237 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1238 @2/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1239 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1240 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1241 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1242
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1243 Or a single *interleaved* dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1244
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1245 @1/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1246 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1247 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1248 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1249 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1250 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1251 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1252 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1253 @2/1
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1254 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1255 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1256 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1257 @2/2
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1258 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1259 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1260 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1261 ]]></help>
2
c1ec08cb34f9 Uploaded
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1262 <citations>
17
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1263 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1264 <citation type="doi">10.1038/nmeth.1923</citation>
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1265 </citations>
0
96d2e31a3938 Imported from capsule None
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diff changeset
1266 </tool>