Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 23:17062a0decb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
author iuc
date Wed, 06 Jun 2018 17:23:32 -0400
parents c3dd1aeb7d07
children 017aba02828d
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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">
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2 <description>- map reads against reference genome</description>
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
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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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
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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15 #set index_path = ''
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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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 = $reference_genome.index.fields.path
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22 #end if
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24 ## Link in the input files, so bowtie2 can tell their type
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26 #set compressed="False"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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27 #set reads_are_fastq = True
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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28 #if str($library.type) == 'paired':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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29 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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
iuc
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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
parents: 17
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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 $library.input_1.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #set reads_are_fastq = False
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iuc
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37 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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38 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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39 #set read1 = "input_f.fastq"
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40 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 ln -f -s '${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"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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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"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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47 #set read2 = "input_r.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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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 $library.input_2.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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50 #set read2 = "input_r.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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51 #else:
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52 #set read2 = "input_r.fastq"
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53 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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54 ln -f -s '${library.input_2}' ${read2} &&
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55 #else if str($library.type) == 'paired_collection':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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56 #if $library.input_1.forward.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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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"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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74 #set read2 = "input_r.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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parents: 17
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75 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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76 #else if $library.input_1.reverse.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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77 #set read2 = "input_r.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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78 #else:
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79 #set read2 = "input_r.fastq"
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80 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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81 ln -s '${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">
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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
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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"/>
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parents: 0
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497 </when>
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parents: 0
diff changeset
498 <when value="no">
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parents: 0
diff changeset
499 <!-- do nothing -->
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parents: 0
diff changeset
500 </when>
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parents: 0
diff changeset
501 </conditional>
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parents: 0
diff changeset
502 <conditional name="other_options">
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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>
c1ec08cb34f9 Uploaded
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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
devteam
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
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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
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parents: 6
diff changeset
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
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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
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parents:
diff changeset
540 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
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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
devteam
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>
23
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iuc
parents: 22
diff changeset
560 <expand macro="dbKeyActions" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
561 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
562 </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
563 <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
564 <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
565 <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
566 <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
567 <when value="single">
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parents: 8
diff changeset
568 <action type="format">
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diff changeset
569 <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
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570 </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
571 </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
572 <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
573 <action type="format">
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parents: 8
diff changeset
574 <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
575 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
576 </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
577 <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
578 <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
579 <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
580 </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
581 </when>
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parents: 8
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582 </conditional>
23
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iuc
parents: 22
diff changeset
583 <expand macro="dbKeyActions" />
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
584 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
585 </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
586 <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
devteam
parents: 8
diff changeset
587 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
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parents: 8
diff changeset
588 <actions>
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parents: 8
diff changeset
589 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
590 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
591 <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
592 <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
593 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
594 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
595 <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
596 <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
597 <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
598 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
599 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
600 </conditional>
23
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iuc
parents: 22
diff changeset
601 <expand macro="dbKeyActions" />
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
602 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
603 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
604 <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
605 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
606 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
607 <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
608 <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
609 <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
610 <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
611 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
612 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
613 <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
614 <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
615 <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
616 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
617 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
618 </conditional>
23
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iuc
parents: 22
diff changeset
619 <expand macro="dbKeyActions" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
620 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
621 </data>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
622 <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
623 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
22
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iuc
parents: 21
diff changeset
624 <change_format>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
625 <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
626 </change_format>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
627 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
628 <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
629 <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
630 <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
631 <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
632 <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
633 <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
devteam
parents: 6
diff changeset
634 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
635 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
636 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
637 <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
638 <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
639 <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
640 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
641 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
642 </conditional>
23
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iuc
parents: 22
diff changeset
643 <expand macro="dbKeyActions" />
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
644 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
645 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
646 <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
647 <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
648 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
649 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
650 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
651 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
652 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
653 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
654 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
655 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
656 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
657 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
658 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
659 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
660 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
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parents:
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661 </action>
96d2e31a3938 Imported from capsule None
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parents:
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662 </when>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
663 </conditional>
23
17062a0decb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents: 22
diff changeset
664 <expand macro="dbKeyActions" />
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
665 </actions>
96d2e31a3938 Imported from capsule None
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diff changeset
666 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
667 <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
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parents: 8
diff changeset
668 <filter>save_mapping_stats is True</filter>
23
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iuc
parents: 22
diff changeset
669 <actions>
17062a0decb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents: 22
diff changeset
670 <expand macro="dbKeyActions" />
17062a0decb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents: 22
diff changeset
671 </actions>
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
672 </data>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
673 </outputs>
96d2e31a3938 Imported from capsule None
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674 <tests>
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675 <test>
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iuc
parents: 16
diff changeset
676 <!-- test on paired-end datasets -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
677 <param name="type" value="paired"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
678 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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diff changeset
679 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
680 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
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diff changeset
681 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
682 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
683 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
684 <param name="own_file" value="bowtie2-ref.fasta" />
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
685 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
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parents:
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686 </test>
5
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devteam
parents: 4
diff changeset
687 <test>
17
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iuc
parents: 16
diff changeset
688 <!-- test on paired collection -->
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
689 <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
690 <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
691 <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
692 <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
693 <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
694 <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
695 <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
696 <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
697 <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
698 </collection>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
699 </param>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
700 <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
701 <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
702 </test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
703 <test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
704 <!-- test on paired-end datasets with read group info -->
5
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="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
706 <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
707 <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
708 <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
709 <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
710 <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
711 <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
712 <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
713 <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
714 <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
715 <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
716 <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
717 </test>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
718 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
719 <!-- 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
720 <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
721 <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
722 <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
723 <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
724 <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
725 <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
726 <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
727 <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
728 <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
729 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 <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
731 <assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
732 <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
733 </assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
734 </output>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
735 </test>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
736 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
737 <!-- 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
738 <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
739 <!-- <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 <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
748 <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
749 </test>
14
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devteam
parents: 13
diff changeset
750 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
751 <!-- 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
752 <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
753 <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
754 <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
755 <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
756 <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
757 <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
758 <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
759 <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
760 <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
761 </test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
762 <test>
17
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iuc
parents: 16
diff changeset
763 <!-- test on fastqsanger.bz2 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
764 <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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 </test>
16
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iuc
parents: 15
diff changeset
774 <test>
17
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iuc
parents: 16
diff changeset
775 <!-- test on fasta paired-end datasets -->
16
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iuc
parents: 15
diff changeset
776 <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
777 <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
778 <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
779 <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
780 <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
781 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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782 <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
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diff changeset
783 <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
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diff changeset
784 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
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785 </test>
22
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diff changeset
786 <test>
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diff changeset
787 <!-- test on fasta paired-end datasets with bam_native as output -->
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788 <param name="type" value="paired"/>
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diff changeset
789 <param name="paired_options_selector" value="no"/>
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790 <param name="unaligned_file" value="false"/>
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791 <param name="analysis_type_selector" value="simple"/>
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diff changeset
792 <param name="source" value="history" />
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793 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
794 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
795 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
796 <param name="sam_options_selector" value="yes" />
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797 <param name="reorder" value="true" />
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798 <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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799 </test>
0
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800 </tests>
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801 <help><![CDATA[
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802 **Bowtie2 Overview**
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803
2
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804 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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805 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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806
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807 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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808 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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809 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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810
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811 -----
0
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812
2
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813 **Selecting reference genomes for Bowtie2**
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814
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815 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
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816
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817 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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818 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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819
2
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820 If your genome of interest is not listed here you have two choices:
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821
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822 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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823 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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824
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825 ------
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826
2
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827 .. class:: infomark
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828
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829 **Bowtie2 options**
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830
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831 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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832
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833 -----
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834
0
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835 **Inputs**
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836
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837 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
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838
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839 ------
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840
2
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841 **Input options**::
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842
15
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843 --interleaved
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844 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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845
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diff changeset
846 -s/--skip <int>
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diff changeset
847 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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848
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diff changeset
849 -u/--qupto <int>
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850 Align the first `<int>` reads or read pairs from the input (after the
2
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851 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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852
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853 -5/--trim5 <int>
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854 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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855
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856 -3/--trim3 <int>
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857 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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858
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859 --phred33
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860 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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861 also called the "Phred+33" encoding, which is used by the very latest Illumina
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862 pipelines.
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863
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864 --phred64
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865 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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866 also called the "Phred+64" encoding.
0
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867
2
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868 --solexa-quals
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869 Convert input qualities from Solexa Phred quality (which can be negative) to
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870 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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871 Pipeline versions (prior to 1.3). Default: off.
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872
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873 --int-quals
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874 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
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875 Integers are treated as being on the Phred quality scale unless
2
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876 `--solexa-quals` is also specified. Default: off.
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877
2
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878 ------
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879
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880 **Presets in `--end-to-end` mode**::
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881
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882 --very-fast
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883 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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884
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885 --fast
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886 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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887
2
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888 --sensitive
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889 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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890
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891 --very-sensitive
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892 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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893
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894 ------
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895
2
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896 **Presets options in `--local` mode**::
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897
2
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898 --very-fast-local
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899 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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900
2
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901 --fast-local
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902 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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903
2
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904 --sensitive-local
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905 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
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906
2
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907 --very-sensitive-local
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908 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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909
0
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910 ------
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911
2
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912 **Alignment options**::
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913
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914 -N <int>
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915 Sets the number of mismatches to allowed in a seed alignment during multiseed
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916 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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917 (often much slower) but increases sensitivity. Default: 0.
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918
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919 -L <int>
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920 Sets the length of the seed substrings to align during multiseed alignment.
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921 Smaller values make alignment slower but more sensitive. Default: the
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diff changeset
922 `--sensitive` preset is used by default, which sets `-L` to 22 in
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diff changeset
923 `--end-to-end` mode and to 20 in `--local` mode.
2
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parents: 0
diff changeset
924
11
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parents: 10
diff changeset
925 -i <func>
2
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parents: 0
diff changeset
926 Sets a function governing the interval between seed substrings to use during
3
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parents: 2
diff changeset
927 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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parents: 0
diff changeset
928 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
929
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parents: 0
diff changeset
930 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
931 Seed 1 fw: TAGCTACGCT
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diff changeset
932 Seed 1 rc: AGCGTAGCTA
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diff changeset
933 Seed 2 fw: CGCTCTACGC
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diff changeset
934 Seed 2 rc: GCGTAGAGCG
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diff changeset
935 Seed 3 fw: ACGCTATCAT
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diff changeset
936 Seed 3 rc: ATGATAGCGT
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diff changeset
937 Seed 4 fw: TCATGCATAA
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diff changeset
938 Seed 4 rc: TTATGCATGA
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diff changeset
939
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parents: 0
diff changeset
940 Since it's best to use longer intervals for longer reads, this parameter sets
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parents: 0
diff changeset
941 the interval as a function of the read length, rather than a single
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parents: 0
diff changeset
942 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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parents: 0
diff changeset
943 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
944 If the function returns a result less than
2
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diff changeset
945 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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parents: 0
diff changeset
946 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
947 in `--local` mode.
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diff changeset
948
11
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parents: 10
diff changeset
949 --n-ceil <func>
2
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parents: 0
diff changeset
950 Sets a function governing the maximum number of ambiguous characters (usually
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parents: 0
diff changeset
951 `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
952 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
953 where x is the read length. Reads exceeding this ceiling are filtered out.
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954 Default: `L,0,0.15`.
2
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diff changeset
955
11
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parents: 10
diff changeset
956 --dpad <int>
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diff changeset
957 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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diff changeset
958 gaps. Default: 15.
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diff changeset
959
11
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parents: 10
diff changeset
960 --gbar <int>
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diff changeset
961 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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962 Default: 4.
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963
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964 --ignore-quals
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965 When calculating a mismatch penalty, always consider the quality value at the
11
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966 mismatched position to be the highest possible, regardless of the actual value.
2
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967 I.e. input is treated as though all quality values are high. This is also the
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968 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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969 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
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970
2
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971 --nofw/--norc
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972 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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973 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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974 not attempt to align unpaired reads against the reverse-complement (Crick)
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diff changeset
975 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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diff changeset
976 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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diff changeset
977 paired-end configurations corresponding to fragments from the reverse-complement
11
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diff changeset
978 (Crick) strand. Default: both strands enabled.
2
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979
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980 --no-1mm-upfront
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981 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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982 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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983 alignments can be found very quickly, and many short read alignments have exact or
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984 near-exact end-to-end alignments. However, this can lead to unexpected
3
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985 alignments when the user also sets options governing the multiseed heuristic,
2
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986 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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987 to the length of the read, the user will be surprised to find 1-mismatch alignments
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988 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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989 alignments before using the multiseed heuristic, which leads to the expected
2
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990 behavior when combined with options such as `-L` and `-N`. This comes at the
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991 expense of speed.
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992
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993 --end-to-end
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994 In this mode, Bowtie 2 requires that the entire read align from one end to the
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995 other, without any trimming (or "soft clipping") of characters from either end.
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996 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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997 are less than or equal to 0, and the greatest possible alignment score is 0.
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998 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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999
2
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1000 --local
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1001 In this mode, Bowtie 2 does not require that the entire read align from one end
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diff changeset
1002 to the other. Rather, some characters may be omitted ("soft clipped") from the
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1003 ends in order to achieve the greatest possible alignment score. The match bonus
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1004 `--ma` is used in this mode, and the best possible alignment score is equal to
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diff changeset
1005 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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1006 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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1007 the local version of the preset (`--very-fast-local`). This is mutually
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diff changeset
1008 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1009
2
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diff changeset
1010 -----
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1011
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diff changeset
1012 **Scoring options**::
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1013
11
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1014 --ma <int>
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1015 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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diff changeset
1016 score for each position where a read character aligns to a reference character
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1017 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1018
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1019 --mp MX,MN
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1020 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1021 number less than or equal to `MX` and greater than or equal to `MN` is
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1022 subtracted from the alignment score for each position where a read character
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1023 aligns to a reference character, the characters do not match, and neither is an
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diff changeset
1024 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1025 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1026 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1027
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diff changeset
1028 --np <int>
2
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1029 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1030 ambiguous character such as `N`. Default: 1.
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1031
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diff changeset
1032 --rdg <int1>,<int2>
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1033 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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diff changeset
1034 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1035
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diff changeset
1036 --rfg <int1>,<int2>
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diff changeset
1037 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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diff changeset
1038 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1039 5, 3.
0
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1040
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diff changeset
1041 --score-min <func>
2
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1042 Sets a function governing the minimum alignment score needed for an alignment to
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1043 be considered "valid" (i.e. good enough to report). This is a function of read
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1044 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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1045 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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diff changeset
1046 the default in `--local` mode is `G,20,8`.
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1047
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diff changeset
1048 -----
2
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1049
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diff changeset
1050 **Reporting options**::
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1051
11
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diff changeset
1052 -k <int>
2
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1053 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1054 When it finds a valid alignment, it continues looking for alignments that are
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1055 nearly as good or better. The best alignment found is reported (randomly
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1056 selected from among best if tied). Information about the best alignments is
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1057 used to estimate mapping quality and to set SAM optional fields, such as
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1058 `AS:i` and `XS:i`.
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1059
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1060 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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1061 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1062 search terminates when it can't find more distinct valid alignments, or when it
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1063 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1064 descending order by alignment score. The alignment score for a paired-end
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1065 alignment equals the sum of the alignment scores of the individual mates. Each
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1066 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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1067 (which equals 256) set in its FLAGS field. For reads that have more than
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1068 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
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1069 `<int>` alignments reported are the best possible in terms of alignment score.
2
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1070 `-k` is mutually exclusive with `-a`.
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1071
2
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1072 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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diff changeset
1073 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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1074
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1075 -a
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diff changeset
1076 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1077 is mutually exclusive with `-k`.
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1078
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diff changeset
1079 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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1080 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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diff changeset
1081
2
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diff changeset
1082 -----
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diff changeset
1083
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diff changeset
1084 **Effort options**::
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diff changeset
1085
11
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diff changeset
1086 -D <int>
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diff changeset
1087 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1088 moves on, using the alignments found so far. A seed extension "fails" if it
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diff changeset
1089 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
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1090 automatically adjusted up when -k or -a are specified. Default: 15.
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diff changeset
1091
11
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diff changeset
1092 -R <int>
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diff changeset
1093 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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diff changeset
1094 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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diff changeset
1095 (same length, same number of mismatches allowed) at different offsets and
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diff changeset
1096 searches for more alignments. A read is considered to have repetitive seeds if
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1097 the total number of seed hits divided by the number of seeds that aligned at
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1098 least once is greater than 300. Default: 2.
11
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diff changeset
1099
2
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diff changeset
1100 -----
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1101
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1102 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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1103
11
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diff changeset
1104 -I/--minins <int>
2
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1105 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1106 specified and a paired-end alignment consists of two 20-bp alignments in the
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1107 appropriate orientation with a 20-bp gap between them, that alignment is
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1108 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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1109 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1110 `-I` constraint is applied with respect to the untrimmed mates.
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1111
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1112 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1113 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1114 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1115 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1116 efficient.
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1117
11
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1118 Default: 0 (essentially imposing no minimum)
2
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1119
11
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diff changeset
1120 -X/--maxins <int>
2
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diff changeset
1121 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1122 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1123 proper orientation with a 60-bp gap between them, that alignment is considered
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1124 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
1125 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1126 constraint is applied with respect to the untrimmed mates, not the trimmed
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1127 mates.
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1128
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1129 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1130 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1131 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1132 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1133 efficient.
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1134
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1135 Default: 500.
0
96d2e31a3938 Imported from capsule None
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1136
2
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1137 --fr/--rf/--ff
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1138 The upstream/downstream mate orientations for a valid paired-end alignment
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1139 against the forward reference strand. E.g., if `--fr` is specified and there is
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1140 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1141 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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diff changeset
1142 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1143 complement of mate 1 and all other constraints are met, that too is valid.
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1144 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1145 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1146 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1147 for Illumina's Paired-end Sequencing Assay).
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1148
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1149 --no-mixed
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1150 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1151 a pair, it then tries to find alignments for the individual mates. This option
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1152 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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1153
2
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1154 --no-discordant
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1155 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1156 concordant alignments. A discordant alignment is an alignment where both mates
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1157 align uniquely, but that does not satisfy the paired-end constraints
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1158 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1159
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1160 --dovetail
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1161 If the mates "dovetail", that is if one mate alignment extends past the
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1162 beginning of the other such that the wrong mate begins upstream, consider that
3
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1163 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1164
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1165 --no-contain
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1166 If one mate alignment contains the other, consider that to be non-concordant.
3
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1167 Default: a mate can contain the other in a concordant alignment.
2
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1168
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1169 --no-overlap
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1170 If one mate alignment overlaps the other at all, consider that to be
3
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1171 non-concordant. Default: mates can overlap in a concordant alignment.
11
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1172
0
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1173 ------
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1174
2
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1175 **SAM options**::
0
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1176
11
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1177 --rg-id <text>
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1178 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1179 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1180 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1181 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
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1182
11
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1183 --rg <text>
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diff changeset
1184 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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diff changeset
1185 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
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1186 must also be specified. This is because the `ID` tag is required by the SAM
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1187 Specification. Specify `--rg` multiple times to set multiple fields. See the
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1188 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
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1189
2
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1190 --omit-sec-seq
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1191 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1192 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1193 in those fields instead.
11
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1194
2
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1195 -----
0
96d2e31a3938 Imported from capsule None
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1196
2
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1197 **Other options**::
0
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1198
2
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1199 --reorder
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1200 Guarantees that output SAM records are printed in an order corresponding to the
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1201 order of the reads in the original input file, even when `-p` is set greater
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1202 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1203 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1204 not specified. Has no effect if `-p` is set to 1, since output order will
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1205 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
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1206
11
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1207 --seed <int>
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1208 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
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1209
2
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1210 --non-deterministic
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1211 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1212 seeds the generator with a number derived from (a) the read name, (b) the
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1213 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1214 option. This means that if two reads are identical (same name, same
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1215 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1216 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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1217 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1218 current time. This means that Bowtie 2 will not necessarily report the same
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1219 alignment for two identical reads. This is counter-intuitive for some users,
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1220 but might be more appropriate in situations where the input consists of many
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1221 identical reads.
0
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1222
15
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1223 -----
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1224
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iuc
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diff changeset
1225
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diff changeset
1226 **Paired-end (and mate-pair) data in fastq format**
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1227
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diff changeset
1228 Paired end datasets can be represented as two individual datasets:
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diff changeset
1229
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diff changeset
1230 First dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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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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diff changeset
1232 @1/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1233 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1234 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1235 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1236 @2/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1237 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1238 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1239 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1240
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1241 Second dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1242
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1243 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1244 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1245 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1246 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1247 @2/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1248 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1249 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1250 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1251
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1252 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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diff changeset
1253
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1254 @1/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1255 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1256 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1257 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1258 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
1259 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1260 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1261 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1262 @2/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1263 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1264 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff changeset
1265 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1266 @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
1267 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1268 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
1269 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
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diff changeset
1270 ]]></help>
2
c1ec08cb34f9 Uploaded
devteam
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diff changeset
1271 <citations>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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diff changeset
1272 <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
iuc
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diff changeset
1273 <citation type="doi">10.1038/nmeth.1923</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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diff changeset
1274 </citations>
0
96d2e31a3938 Imported from capsule None
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diff changeset
1275 </tool>