Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 18:121110a12cc9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
author iuc
date Fri, 24 Nov 2017 07:44:07 -0500
parents 66f992977578
children 97d1923c8c4b
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121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.3.1" profile="17.01">
2
c1ec08cb34f9 Uploaded
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2 <description>- map reads against reference genome</description>
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
5
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5 </macros>
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6 <requirements>
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parents: 17
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7 <requirement type="package" version="2.3.3.1">bowtie2</requirement>
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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8 <requirement type="package" version="1.6">samtools</requirement>
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b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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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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iuc
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12 ## prepare bowtie2 index
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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13 #set index_path = ''
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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14 #if str($reference_genome.source) == "history":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$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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16 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
iuc
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17 #set index_path = 'genome'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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18 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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19 #set index_path = $reference_genome.index.fields.path
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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20 #end if
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121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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22 ## Link in the input files, so bowtie2 can tell their type
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121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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24 #set compressed="False"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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25 #set reads_are_fastq = True
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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26 #if str($library.type) == 'paired':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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27 #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
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28 #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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29 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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30 #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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31 #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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32 #set compressed = "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 #else if $library.input_1.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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34 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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35 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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36 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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37 #set read1 = "input_f.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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38 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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39 ln -f -s '${library.input_1}' ${read1} &&
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41 #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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42 #set read2 = "input_r.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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43 #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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44 #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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45 #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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46 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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47 #else if $library.input_2.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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48 #set read2 = "input_r.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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49 #else:
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50 #set read2 = "input_r.fastq"
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51 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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52 ln -f -s '${library.input_2}' ${read2} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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53 #else if str($library.type) == 'paired_collection':
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54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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55 #set read1 = "input_f.fastq.gz"
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56 #set compressed = "GZ"
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57 #else if $library.input_1.forward.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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58 #set read1 = "input_f.fastq.bz2"
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59 #set compressed = "BZ2"
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60 #else if $library.input_1.forward.is_of_type('fasta'):
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61 #set reads_are_fastq = False
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62 #set read1 = "input_f.fasta"
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63 #else:
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64 #set read1 = "input_f.fastq"
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65 #end if
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66 ln -s '${library.input_1.forward}' ${read1} &&
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67
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68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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69 #set read2 = "input_r.fastq.gz"
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70 #set compressed = "GZ"
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71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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72 #set read2 = "input_r.fastq.bz2"
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73 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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74 #else if $library.input_1.reverse.is_of_type("fasta"):
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75 #set read2 = "input_r.fasta"
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76 #else:
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77 #set read2 = "input_r.fastq"
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78 #end if
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79 ln -s '${library.input_1.reverse}' ${read2} &&
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43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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80
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81 #else if str($library.type) == 'paired_interleaved':
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82 #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
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83 #set read1 = "input_il.fastq.gz"
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84 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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85 #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
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86 #set read1 = "input_il.fastq.bz2"
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iuc
parents: 17
diff changeset
87 #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
88 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
89 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #set read1 = "input_il.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
91 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
92 #set read1 = "input_il.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
94 ln -s '${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
95 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
96 #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
97 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
98 #set compressed = "GZ"
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iuc
parents: 17
diff changeset
99 #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
100 #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
101 #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
102 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
103 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
104 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set read1 = "input_f.fastq"
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iuc
parents: 17
diff changeset
107 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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108 ln -s '${library.input_1}' ${read1} &&
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iuc
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diff changeset
109 #end if
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diff changeset
110
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111 ## execute bowtie2
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iuc
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diff changeset
112
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113 bowtie2
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114
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diff changeset
115 ## number of threads
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116 -p \${GALAXY_SLOTS:-4}
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117
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118 ## index file path
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iuc
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119 -x '$index_path'
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120
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121 ## Input reads are fasta?
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iuc
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122 #if not reads_are_fastq:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
123 -f
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iuc
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diff changeset
124 #end if
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125
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diff changeset
126 ## Input reads
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iuc
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127 #if str( $library.type ) == "single":
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128 -U '${read1}'
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iuc
parents: 17
diff changeset
129 #if str( $library.unaligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
130 #if $compressed == "GZ":
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iuc
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diff changeset
131 --un-gz '${output_unaligned_reads_l}'
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iuc
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diff changeset
132 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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133 --un-bz2 '${output_unaligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
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diff changeset
134 #else:
18
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135 --un '${output_unaligned_reads_l}'
14
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devteam
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diff changeset
136 #end if
18
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iuc
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diff changeset
137 #end if
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iuc
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diff changeset
138 #if str( $library.aligned_file ) == "true":
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iuc
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diff changeset
139 #if $compressed == "GZ":
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iuc
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diff changeset
140 --al-gz '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
141 #else if $compressed == "BZ2":
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iuc
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diff changeset
142 --al-bz2 '${output_aligned_reads_l}'
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iuc
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diff changeset
143 #else:
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144 --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
145 #end if
18
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146 #end if
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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147
18
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148 #elif str( $library.type ) == "paired_interleaved":
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149 --interleaved '${read1}'
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150 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
151 #if $compressed == "GZ":
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diff changeset
152 --un-gz '${output_unaligned_reads_l}'
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iuc
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153 #else if $compressed == "BZ2":
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iuc
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diff changeset
154 --un-bz2 '${output_unaligned_reads_l}'
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iuc
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diff changeset
155 #else:
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iuc
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diff changeset
156 --un '${output_unaligned_reads_l}'
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iuc
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diff changeset
157 #end if
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diff changeset
158 #end if
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159 #if str( $library.aligned_file ) == "true":
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diff changeset
160 #if $compressed == "GZ":
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iuc
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diff changeset
161 --al-gz '${output_aligned_reads_l}'
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iuc
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diff changeset
162 #else if $compressed == "BZ2":
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iuc
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diff changeset
163 --al-bz2 '${output_aligned_reads_l}'
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iuc
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diff changeset
164 #else:
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165 --al '${output_aligned_reads_l}'
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iuc
parents: 17
diff changeset
166 #end if
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iuc
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diff changeset
167 #end if
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diff changeset
168 #else:
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diff changeset
169 -1 '${read1}'
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iuc
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diff changeset
170 -2 '${read2}'
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iuc
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171 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
172 #if $compressed == "GZ":
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iuc
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diff changeset
173 --un-conc-gz '${output_unaligned_reads_l}'
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iuc
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diff changeset
174 #else if $compressed == "BZ2":
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iuc
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diff changeset
175 --un-conc-bz2 '${output_unaligned_reads_l}'
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iuc
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diff changeset
176 #else:
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diff changeset
177 --un-conc '${output_unaligned_reads_l}'
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178 #end if
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179 #end if
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180 #if str( $library.aligned_file ) == "true":
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181 #if $compressed == "GZ":
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182 --al-conc-gz '${output_aligned_reads_l}'
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183 #else if $compressed == "BZ2":
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184 --al-conc-bz2 '${output_aligned_reads_l}'
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185 #else:
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186 --al-conc '${output_aligned_reads_l}'
0
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187 #end if
18
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188 #end if
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189 #if str( $library.paired_options.paired_options_selector ) == "yes":
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190 -I ${library.paired_options.I}
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191 -X ${library.paired_options.X}
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192 ${library.paired_options.fr_rf_ff}
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193 ${library.paired_options.no_mixed}
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194 ${library.paired_options.no_discordant}
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195 ${library.paired_options.dovetail}
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196 ${library.paired_options.no_contain}
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197 ${library.paired_options.no_overlap}
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198 #end if
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199 #end if
7
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200
18
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201 ## Read group information.
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202 @define_read_group_helpers@
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203 #if str( $library.type ) == "single":
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204 #set $rg_auto_name = $read_group_name_default($library.input_1)
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205 #elif str( $library.type ) == "paired":
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206 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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207 #else
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208 #set $rg_auto_name = $read_group_name_default($library.input_1)
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209 #end if
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210 @set_use_rg_var@
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211 @set_read_group_vars@
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212 #if $use_rg
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213 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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215 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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216 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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217 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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218 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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219 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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220 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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221 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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222 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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223 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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224 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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225 #end if
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226
18
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227 ## Analysis type
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228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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229 $analysis_type.presets
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230 #elif str( $analysis_type.analysis_type_selector ) == "full":
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231 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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232 --skip ${analysis_type.input_options.skip}
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233 --qupto ${analysis_type.input_options.qupto}
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234 --trim5 ${analysis_type.input_options.trim5}
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235 --trim3 ${analysis_type.input_options.trim3}
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236 ${analysis_type.input_options.qv_encoding}
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237 ${analysis_type.input_options.solexa_quals}
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238 ${analysis_type.input_options.int_quals}
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239 #end if
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240
18
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241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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242 -N ${analysis_type.alignment_options.N}
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243 -L ${analysis_type.alignment_options.L}
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244 -i '${analysis_type.alignment_options.i}'
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245 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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246 --dpad ${analysis_type.alignment_options.dpad}
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247 --gbar ${analysis_type.alignment_options.gbar}
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248 ${analysis_type.alignment_options.ignore_quals}
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249 ${analysis_type.alignment_options.nofw}
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250 ${analysis_type.alignment_options.norc}
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251 ${analysis_type.alignment_options.no_1mm_upfront}
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252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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253 --end-to-end
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254 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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256 --local
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257 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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258 #end if
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259 #end if
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260
18
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261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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262 #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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263 --ma ${analysis_type.scoring_options.ma}
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264 #end if
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265 --mp '${analysis_type.scoring_options.mp}'
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266 --np ${analysis_type.scoring_options.np}
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267 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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268 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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269 #end if
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270
18
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271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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272 -k ${analysis_type.reporting_options.k}
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273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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274 -a
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275 #end if
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276
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277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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278 -D ${analysis_type.effort_options.D}
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279 -R ${analysis_type.effort_options.R}
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280 #end if
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281
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282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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283 ${analysis_type.sam_options.no_unal}
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284 ${analysis_type.sam_options.omit_sec_seq}
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285 ${analysis_type.sam_options.sam-no-qname-trunc}
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286 ${analysis_type.sam_options.xeq}
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287 ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
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288 #end if
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289
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290 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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291 ${analysis_type.other_options.reorder}
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292 ${analysis_type.other_options.non_deterministic}
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293 --seed ${analysis_type.other_options.seed}
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294 #end if
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295
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296 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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297 ${analysis_type.cline}
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298 #end if
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299
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300 ## mapping stats (i.e. stderr from bowtie2)
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301 #if $save_mapping_stats
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302 2> '$mapping_stats'
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303 #end if
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304
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305 ## output file
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306 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
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307 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
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308 #else
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309 > '$output_sam'
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310 #end if
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311
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312 ## rename unaligned sequence files
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313 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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314 #from os.path import splitext
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315 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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316 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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317 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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318 #end if
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319 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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320 #from os.path import splitext
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321 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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322 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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323 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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324 #end if
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325
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326 ]]></command>
0
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327 <inputs>
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328 <!-- single/paired -->
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329 <conditional name="library">
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330 <param name="type" type="select" label="Is this single or paired library">
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331 <option value="single">Single-end</option>
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332 <option value="paired">Paired-end</option>
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333 <option value="paired_collection">Paired-end Dataset Collection</option>
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334 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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335 </param>
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336
0
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337 <when value="single">
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338 <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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339 <expand macro="align_unalign" />
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340 </when>
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341 <when value="paired">
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342 <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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343 <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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344 <expand macro="align_unalign" />
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345 <expand macro="paired_end_options" />
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346 </when>
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347 <when value="paired_collection">
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348 <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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349 <expand macro="align_unalign" />
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350 <expand macro="paired_end_options" />
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351 </when>
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352 <when value="paired_interleaved">
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353 <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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354 <expand macro="align_unalign" />
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355 <expand macro="paired_end_options" />
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356 </when>
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357 </conditional>
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358 <!-- reference genome -->
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359 <conditional name="reference_genome">
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360 <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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361 <option value="indexed">Use a built-in genome index</option>
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362 <option value="history">Use a genome from the history and build index</option>
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363 </param>
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364 <when value="indexed">
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365 <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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366 <options from_data_table="bowtie2_indexes">
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367 <filter type="sort_by" column="2"/>
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368 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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369 </options>
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370 </param>
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371 </when>
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372 <when value="history">
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373 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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374 </when>
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375 </conditional>
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376 <!-- read group settings -->
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377 <expand macro="read_group_conditional" />
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378 <conditional name="analysis_type">
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379 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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380 <option value="simple">1: Default setting only</option>
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381 <option value="full">2: Full parameter list</option>
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382 </param>
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383 <when value="simple">
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384 <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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385 <option value="no_presets" selected="True">No, just use defaults</option>
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386 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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387 <option value="--fast">Fast end-to-end (--fast)</option>
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388 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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389 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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390 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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391 <option value="--fast-local">Fast local (--fast-local)</option>
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392 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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393 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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394 </param>
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395 </when>
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396 <when value="full">
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397 <conditional name="input_options">
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398 <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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399 <option value="yes">Yes</option>
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400 <option value="no" selected="true">No</option>
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401 </param>
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402 <when value="yes">
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403 <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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404 <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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405 <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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406 <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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407 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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408 <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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409 <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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410 </param>
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411 <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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412 <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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413 </when>
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414 <when value="no">
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415 <!-- do nothing -->
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416 </when>
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417 </conditional>
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418 <conditional name="alignment_options">
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419 <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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420 <option value="yes">Yes</option>
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421 <option value="no" selected="true">No</option>
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422 </param>
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423 <when value="yes">
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424 <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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425 <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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426 <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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427 <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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428 <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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429 <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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430 <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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431 <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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432 <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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433 <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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434 <conditional name="align_mode">
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435 <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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436 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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437 <option value="local">Local (--local)</option>
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438 </param>
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439 <when value="end-to-end">
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440 <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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441 </when>
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442 <when value="local">
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443 <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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444 </when>
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445 </conditional>
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446 </when>
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447 <when value="no">
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448 <!-- do nothing -->
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449 </when>
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450 </conditional>
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451 <conditional name="scoring_options">
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452 <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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453 <option value="yes">Yes</option>
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454 <option value="no" selected="true">No</option>
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455 </param>
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456 <when value="yes">
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457 <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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458 <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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459 <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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460 <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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461 <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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462 <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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463 <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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464 </when>
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465 <when value="no">
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466 <!-- do nothing -->
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467 </when>
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468 </conditional>
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469 <conditional name="reporting_options">
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470 <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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471 <option value="no" selected="true">No, do not set</option>
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472 <option value="k">Set -k option and enter -k value</option>
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473 <option value="a">Set -a option</option>
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474 </param>
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475 <when value="no">
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476 <!-- do nothing -->
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477 </when>
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478 <when value="k">
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479 <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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480 </when>
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481 <when value="a">
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482 <!-- do nothing here; set -a flag on the command line-->
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483 </when>
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484 </conditional>
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485 <conditional name="effort_options">
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486 <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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487 <option value="yes">Yes</option>
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488 <option value="no" selected="true">No</option>
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489 </param>
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490 <when value="yes">
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491 <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
492 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
493 </when>
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parents: 0
diff changeset
494 <when value="no">
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parents: 0
diff changeset
495 <!-- do nothing -->
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
496 </when>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
497 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
498 <conditional name="sam_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
499 <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">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
500 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
501 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
502 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
503 <when value="yes">
3
ceb6467e276c Uploaded
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parents: 2
diff changeset
504 <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"/>
ceb6467e276c Uploaded
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parents: 2
diff changeset
505 <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"/>
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
506 <param 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"/>
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
508 <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
509 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
510 <when value="no">
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
511 <!-- do nothing -->
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
512 </when>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
513 </conditional>
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parents: 0
diff changeset
514 <conditional name="other_options">
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
515 <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
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parents: 0
diff changeset
516 <option value="yes">Yes</option>
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parents: 0
diff changeset
517 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
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parents: 0
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518 </param>
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parents: 0
diff changeset
519 <when value="yes">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
520 <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" help="--reorder; Default=False"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
521 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
3
ceb6467e276c Uploaded
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parents: 2
diff changeset
522 <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
523 </when>
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devteam
parents: 0
diff changeset
524 <when value="no">
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parents: 0
diff changeset
525 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
526 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
527 </conditional>
7
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
528 <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."/>
0
96d2e31a3938 Imported from capsule None
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529 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
530 </conditional>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
531 <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
532 </inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
533 <!-- define outputs -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
534 <outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
535 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
536 <filter>library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
537 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
538 <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
539 <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
540 <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
541 <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
542 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
543 </when>
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="paired">
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_collection">
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="forward.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 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
555 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
556 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
557 <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
558 <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
559 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
560 <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
561 <when value="single">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
562 <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
563 <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
devteam
parents: 8
diff changeset
564 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
565 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
566 <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
567 <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
568 <option type="from_param" name="library.input_1" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
569 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
570 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
571 <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
572 <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
573 <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
devteam
parents: 8
diff changeset
574 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
575 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
576 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
577 </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
578 </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
579 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
580 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
581 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
582 <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
583 <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
584 <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
585 <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
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parents: 8
diff changeset
586 </action>
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devteam
parents: 8
diff changeset
587 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
588 <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
589 <action type="format">
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devteam
parents: 8
diff changeset
590 <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
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parents: 8
diff changeset
591 </action>
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devteam
parents: 8
diff changeset
592 </when>
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diff changeset
593 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
594 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
595 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
596 <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
597 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
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598 <actions>
7
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devteam
parents: 6
diff changeset
599 <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
600 <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
601 <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
602 <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
603 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
604 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
605 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
606 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
607 <option type="from_param" name="library.input_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
608 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
609 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
610 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
611 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
612 </data>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
613 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
614 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
615 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
616 <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
617 <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
618 <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
619 <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
620 <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
621 <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
622 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
623 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
624 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
625 <when value="history">
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devteam
parents: 6
diff changeset
626 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
627 <option type="from_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
628 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
629 </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
630 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
631 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
632 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
633 <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
634 <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
635 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
636 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
637 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
638 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
639 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
640 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
641 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
642 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
643 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
644 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
645 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
646 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
647 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
648 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
649 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
650 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
651 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
652 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
653 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
654 <filter>save_mapping_stats is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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655 </data>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
656 </outputs>
96d2e31a3938 Imported from capsule None
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parents:
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657 <tests>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
658 <test>
17
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iuc
parents: 16
diff changeset
659 <!-- test on paired-end datasets -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
660 <param name="type" value="paired"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
661 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
662 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
663 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
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parents:
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664 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
665 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
666 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
667 <param name="own_file" value="bowtie2-ref.fasta" />
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devteam
parents: 0
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668 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
669 </test>
5
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devteam
parents: 4
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670 <test>
17
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iuc
parents: 16
diff changeset
671 <!-- 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
672 <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
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 <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
681 </collection>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 </param>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
683 <param name="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
684 <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
685 </test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <!-- test on paired-end datasets with read group info -->
5
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parents: 4
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688 <param name="type" value="paired"/>
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parents: 4
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689 <param name="paired_options_selector" value="no"/>
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parents: 4
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690 <param name="unaligned_file" value="false"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
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691 <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
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parents: 4
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692 <param name="rg_selector" value="set"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
diff changeset
693 <param name="ID" value="rg1"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
diff changeset
694 <param name="PL" value="CAPILLARY"/>
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parents: 4
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695 <param name="source" value="history" />
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devteam
parents: 4
diff changeset
696 <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
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parents: 4
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697 <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
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parents: 4
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698 <param name="own_file" value="bowtie2-ref.fasta" />
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devteam
parents: 4
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699 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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parents: 4
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700 </test>
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parents: 8
diff changeset
701 <test>
17
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iuc
parents: 16
diff changeset
702 <!-- test on paired-end datasets with stats output -->
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parents: 8
diff changeset
703 <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
704 <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
705 <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
706 <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
707 <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
708 <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
709 <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
710 <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
711 <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
712 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
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iuc
parents: 14
diff changeset
713 <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
714 <assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
715 <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
716 </assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
717 </output>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
718 </test>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
719 <test>
17
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iuc
parents: 16
diff changeset
720 <!-- 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
721 <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
722 <!-- <param name="paired_options_selector" value="no"/> -->
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
723 <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
724 <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
725 <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
726 <param name="ID" value="rg1"/>
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
727 <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
728 <param name="source" value="history" />
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
729 <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
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parents: 14
diff changeset
730 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 14
diff changeset
731 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
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diff changeset
732 </test>
14
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diff changeset
733 <test>
17
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diff changeset
734 <!-- test on fastqsanger.gz paired-end datasets -->
14
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diff changeset
735 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
736 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
737 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
738 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
739 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
740 <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
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parents: 13
diff changeset
741 <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
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diff changeset
742 <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
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diff changeset
743 <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
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diff changeset
744 </test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
745 <test>
17
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parents: 16
diff changeset
746 <!-- 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
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diff changeset
747 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
748 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
749 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
750 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
751 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
752 <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
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diff changeset
753 <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
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parents: 13
diff changeset
754 <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
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parents: 13
diff changeset
755 <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
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diff changeset
756 </test>
16
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iuc
parents: 15
diff changeset
757 <test>
17
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parents: 16
diff changeset
758 <!-- test on fasta paired-end datasets -->
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
759 <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
760 <param name="paired_options_selector" value="no"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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parents: 15
diff changeset
761 <param name="unaligned_file" value="false"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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parents: 15
diff changeset
762 <param name="analysis_type_selector" value="simple"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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parents: 15
diff changeset
763 <param name="source" value="history" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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diff changeset
764 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
765 <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
766 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
767 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
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diff changeset
768 </test>
0
96d2e31a3938 Imported from capsule None
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diff changeset
769 </tests>
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770 <help><![CDATA[
0
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771 **Bowtie2 Overview**
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772
2
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773 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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774 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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775
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776 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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777 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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778 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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779
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780 -----
0
96d2e31a3938 Imported from capsule None
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781
2
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782 **Selecting reference genomes for Bowtie2**
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783
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784 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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785
11
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786 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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787 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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788
2
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diff changeset
789 If your genome of interest is not listed here you have two choices:
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790
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791 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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792 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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793
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794 ------
96d2e31a3938 Imported from capsule None
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795
2
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796 .. class:: infomark
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797
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798 **Bowtie2 options**
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799
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800 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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801
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802 -----
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803
0
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804 **Inputs**
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805
15
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parents: 14
diff changeset
806 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
0
96d2e31a3938 Imported from capsule None
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807
96d2e31a3938 Imported from capsule None
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808 ------
96d2e31a3938 Imported from capsule None
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809
2
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810 **Input options**::
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diff changeset
811
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diff changeset
812 --interleaved
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813 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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diff changeset
814
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diff changeset
815 -s/--skip <int>
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diff changeset
816 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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817
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diff changeset
818 -u/--qupto <int>
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diff changeset
819 Align the first `<int>` reads or read pairs from the input (after the
2
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820 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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diff changeset
821
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diff changeset
822 -5/--trim5 <int>
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823 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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96d2e31a3938 Imported from capsule None
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824
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825 -3/--trim3 <int>
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826 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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827
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828 --phred33
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829 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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830 also called the "Phred+33" encoding, which is used by the very latest Illumina
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831 pipelines.
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832
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833 --phred64
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834 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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835 also called the "Phred+64" encoding.
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836
2
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837 --solexa-quals
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838 Convert input qualities from Solexa Phred quality (which can be negative) to
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839 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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840 Pipeline versions (prior to 1.3). Default: off.
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841
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842 --int-quals
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843 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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844 Integers are treated as being on the Phred quality scale unless
2
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845 `--solexa-quals` is also specified. Default: off.
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846
2
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847 ------
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848
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849 **Presets in `--end-to-end` mode**::
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850
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851 --very-fast
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diff changeset
852 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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853
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854 --fast
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diff changeset
855 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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diff changeset
856
2
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857 --sensitive
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858 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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859
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860 --very-sensitive
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861 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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96d2e31a3938 Imported from capsule None
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862
96d2e31a3938 Imported from capsule None
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863 ------
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864
2
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865 **Presets options in `--local` mode**::
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866
2
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867 --very-fast-local
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diff changeset
868 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
96d2e31a3938 Imported from capsule None
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869
2
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870 --fast-local
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871 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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872
2
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873 --sensitive-local
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874 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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875
2
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876 --very-sensitive-local
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877 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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878
0
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879 ------
96d2e31a3938 Imported from capsule None
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880
2
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diff changeset
881 **Alignment options**::
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882
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diff changeset
883 -N <int>
3
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884 Sets the number of mismatches to allowed in a seed alignment during multiseed
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diff changeset
885 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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886 (often much slower) but increases sensitivity. Default: 0.
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diff changeset
887
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diff changeset
888 -L <int>
3
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889 Sets the length of the seed substrings to align during multiseed alignment.
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diff changeset
890 Smaller values make alignment slower but more sensitive. Default: the
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891 `--sensitive` preset is used by default, which sets `-L` to 22 in
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892 `--end-to-end` mode and to 20 in `--local` mode.
2
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diff changeset
893
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diff changeset
894 -i <func>
2
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895 Sets a function governing the interval between seed substrings to use during
3
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896 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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897 length is 10, and the seed interval is 6, the seeds extracted will be:
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898
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diff changeset
899 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
900 Seed 1 fw: TAGCTACGCT
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diff changeset
901 Seed 1 rc: AGCGTAGCTA
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diff changeset
902 Seed 2 fw: CGCTCTACGC
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diff changeset
903 Seed 2 rc: GCGTAGAGCG
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diff changeset
904 Seed 3 fw: ACGCTATCAT
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diff changeset
905 Seed 3 rc: ATGATAGCGT
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diff changeset
906 Seed 4 fw: TCATGCATAA
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diff changeset
907 Seed 4 rc: TTATGCATGA
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diff changeset
908
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diff changeset
909 Since it's best to use longer intervals for longer reads, this parameter sets
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diff changeset
910 the interval as a function of the read length, rather than a single
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diff changeset
911 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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diff changeset
912 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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diff changeset
913 If the function returns a result less than
2
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914 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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915 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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916 in `--local` mode.
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diff changeset
917
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diff changeset
918 --n-ceil <func>
2
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diff changeset
919 Sets a function governing the maximum number of ambiguous characters (usually
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diff changeset
920 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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diff changeset
921 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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diff changeset
922 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
923 Default: `L,0,0.15`.
2
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diff changeset
924
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diff changeset
925 --dpad <int>
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926 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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927 gaps. Default: 15.
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928
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diff changeset
929 --gbar <int>
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diff changeset
930 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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931 Default: 4.
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932
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933 --ignore-quals
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diff changeset
934 When calculating a mismatch penalty, always consider the quality value at the
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935 mismatched position to be the highest possible, regardless of the actual value.
2
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936 I.e. input is treated as though all quality values are high. This is also the
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937 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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938 `-r`, or `-c` modes).
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939
2
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940 --nofw/--norc
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941 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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942 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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943 not attempt to align unpaired reads against the reverse-complement (Crick)
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diff changeset
944 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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945 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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946 paired-end configurations corresponding to fragments from the reverse-complement
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947 (Crick) strand. Default: both strands enabled.
2
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948
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949 --no-1mm-upfront
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950 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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951 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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952 alignments can be found very quickly, and many short read alignments have exact or
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953 near-exact end-to-end alignments. However, this can lead to unexpected
3
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954 alignments when the user also sets options governing the multiseed heuristic,
2
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955 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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956 to the length of the read, the user will be surprised to find 1-mismatch alignments
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957 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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958 alignments before using the multiseed heuristic, which leads to the expected
2
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959 behavior when combined with options such as `-L` and `-N`. This comes at the
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960 expense of speed.
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961
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962 --end-to-end
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963 In this mode, Bowtie 2 requires that the entire read align from one end to the
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964 other, without any trimming (or "soft clipping") of characters from either end.
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diff changeset
965 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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966 are less than or equal to 0, and the greatest possible alignment score is 0.
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967 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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968
2
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969 --local
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diff changeset
970 In this mode, Bowtie 2 does not require that the entire read align from one end
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diff changeset
971 to the other. Rather, some characters may be omitted ("soft clipped") from the
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diff changeset
972 ends in order to achieve the greatest possible alignment score. The match bonus
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diff changeset
973 `--ma` is used in this mode, and the best possible alignment score is equal to
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parents: 0
diff changeset
974 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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975 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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976 the local version of the preset (`--very-fast-local`). This is mutually
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diff changeset
977 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
11
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978
2
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parents: 0
diff changeset
979 -----
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980
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diff changeset
981 **Scoring options**::
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982
11
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parents: 10
diff changeset
983 --ma <int>
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diff changeset
984 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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diff changeset
985 score for each position where a read character aligns to a reference character
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diff changeset
986 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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parents: 0
diff changeset
987
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diff changeset
988 --mp MX,MN
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diff changeset
989 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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diff changeset
990 number less than or equal to `MX` and greater than or equal to `MN` is
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diff changeset
991 subtracted from the alignment score for each position where a read character
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diff changeset
992 aligns to a reference character, the characters do not match, and neither is an
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diff changeset
993 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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994 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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diff changeset
995 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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996
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diff changeset
997 --np <int>
2
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diff changeset
998 Sets penalty for positions where the read, reference, or both, contain an
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parents: 0
diff changeset
999 ambiguous character such as `N`. Default: 1.
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parents: 0
diff changeset
1000
11
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parents: 10
diff changeset
1001 --rdg <int1>,<int2>
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diff changeset
1002 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1003 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1004
11
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parents: 10
diff changeset
1005 --rfg <int1>,<int2>
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diff changeset
1006 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1007 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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1008 5, 3.
0
96d2e31a3938 Imported from capsule None
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1009
11
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diff changeset
1010 --score-min <func>
2
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1011 Sets a function governing the minimum alignment score needed for an alignment to
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1012 be considered "valid" (i.e. good enough to report). This is a function of read
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1013 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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1014 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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1015 the default in `--local` mode is `G,20,8`.
11
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diff changeset
1016
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diff changeset
1017 -----
2
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1018
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diff changeset
1019 **Reporting options**::
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1020
11
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diff changeset
1021 -k <int>
2
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diff changeset
1022 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1023 When it finds a valid alignment, it continues looking for alignments that are
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1024 nearly as good or better. The best alignment found is reported (randomly
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parents: 0
diff changeset
1025 selected from among best if tied). Information about the best alignments is
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1026 used to estimate mapping quality and to set SAM optional fields, such as
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diff changeset
1027 `AS:i` and `XS:i`.
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1028
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1029 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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diff changeset
1030 searches for at most `<int>` distinct, valid alignments for each read. The
2
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diff changeset
1031 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
1032 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1033 descending order by alignment score. The alignment score for a paired-end
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1034 alignment equals the sum of the alignment scores of the individual mates. Each
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diff changeset
1035 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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diff changeset
1036 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1037 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1038 `<int>` alignments reported are the best possible in terms of alignment score.
2
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1039 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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1040
2
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1041 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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diff changeset
1042 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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1043
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1044 -a
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1045 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1046 is mutually exclusive with `-k`.
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1047
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1048 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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diff changeset
1049 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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1050
2
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diff changeset
1051 -----
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1052
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1053 **Effort options**::
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1054
11
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1055 -D <int>
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diff changeset
1056 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1057 moves on, using the alignments found so far. A seed extension "fails" if it
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1058 does not yield a new best or a new second-best alignment. This limit is
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1059 automatically adjusted up when -k or -a are specified. Default: 15.
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1060
11
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1061 -R <int>
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1062 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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1063 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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1064 (same length, same number of mismatches allowed) at different offsets and
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1065 searches for more alignments. A read is considered to have repetitive seeds if
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1066 the total number of seed hits divided by the number of seeds that aligned at
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1067 least once is greater than 300. Default: 2.
11
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1068
2
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diff changeset
1069 -----
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1070
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1071 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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1072
11
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1073 -I/--minins <int>
2
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1074 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1075 specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1076 appropriate orientation with a 20-bp gap between them, that alignment is
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1077 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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1078 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1079 `-I` constraint is applied with respect to the untrimmed mates.
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1080
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diff changeset
1081 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1082 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1083 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1084 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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diff changeset
1085 efficient.
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1086
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1087 Default: 0 (essentially imposing no minimum)
2
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1088
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diff changeset
1089 -X/--maxins <int>
2
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1090 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1091 is specified and a paired-end alignment consists of two 20-bp alignments in the
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1092 proper orientation with a 60-bp gap between them, that alignment is considered
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1093 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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1094 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1095 constraint is applied with respect to the untrimmed mates, not the trimmed
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1096 mates.
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diff changeset
1097
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diff changeset
1098 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1099 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1100 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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parents: 0
diff changeset
1101 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1102 efficient.
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1103
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1104 Default: 500.
0
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1105
2
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1106 --fr/--rf/--ff
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1107 The upstream/downstream mate orientations for a valid paired-end alignment
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1108 against the forward reference strand. E.g., if `--fr` is specified and there is
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1109 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1110 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1111 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1112 complement of mate 1 and all other constraints are met, that too is valid.
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1113 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1114 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1115 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1116 for Illumina's Paired-end Sequencing Assay).
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1117
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1118 --no-mixed
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diff changeset
1119 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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diff changeset
1120 a pair, it then tries to find alignments for the individual mates. This option
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diff changeset
1121 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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diff changeset
1122
2
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diff changeset
1123 --no-discordant
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diff changeset
1124 By default, `bowtie2` looks for discordant alignments if it cannot find any
c1ec08cb34f9 Uploaded
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diff changeset
1125 concordant alignments. A discordant alignment is an alignment where both mates
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diff changeset
1126 align uniquely, but that does not satisfy the paired-end constraints
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diff changeset
1127 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1128
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diff changeset
1129 --dovetail
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diff changeset
1130 If the mates "dovetail", that is if one mate alignment extends past the
c1ec08cb34f9 Uploaded
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diff changeset
1131 beginning of the other such that the wrong mate begins upstream, consider that
3
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diff changeset
1132 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1133
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diff changeset
1134 --no-contain
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diff changeset
1135 If one mate alignment contains the other, consider that to be non-concordant.
3
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diff changeset
1136 Default: a mate can contain the other in a concordant alignment.
2
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1137
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1138 --no-overlap
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diff changeset
1139 If one mate alignment overlaps the other at all, consider that to be
3
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diff changeset
1140 non-concordant. Default: mates can overlap in a concordant alignment.
11
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diff changeset
1141
0
96d2e31a3938 Imported from capsule None
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diff changeset
1142 ------
96d2e31a3938 Imported from capsule None
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diff changeset
1143
2
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diff changeset
1144 **SAM options**::
0
96d2e31a3938 Imported from capsule None
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diff changeset
1145
11
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diff changeset
1146 --rg-id <text>
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diff changeset
1147 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1148 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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diff changeset
1149 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1150 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
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diff changeset
1151
11
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diff changeset
1152 --rg <text>
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diff changeset
1153 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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diff changeset
1154 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
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diff changeset
1155 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1156 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1157 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
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1158
2
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diff changeset
1159 --omit-sec-seq
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diff changeset
1160 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
c1ec08cb34f9 Uploaded
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diff changeset
1161 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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diff changeset
1162 in those fields instead.
11
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diff changeset
1163
2
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diff changeset
1164 -----
0
96d2e31a3938 Imported from capsule None
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1165
2
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diff changeset
1166 **Other options**::
0
96d2e31a3938 Imported from capsule None
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1167
2
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diff changeset
1168 --reorder
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diff changeset
1169 Guarantees that output SAM records are printed in an order corresponding to the
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diff changeset
1170 order of the reads in the original input file, even when `-p` is set greater
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diff changeset
1171 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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diff changeset
1172 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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diff changeset
1173 not specified. Has no effect if `-p` is set to 1, since output order will
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diff changeset
1174 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
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diff changeset
1175
11
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diff changeset
1176 --seed <int>
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diff changeset
1177 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
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1178
2
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diff changeset
1179 --non-deterministic
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diff changeset
1180 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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diff changeset
1181 seeds the generator with a number derived from (a) the read name, (b) the
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diff changeset
1182 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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diff changeset
1183 option. This means that if two reads are identical (same name, same
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diff changeset
1184 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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diff changeset
1185 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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diff changeset
1186 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1187 current time. This means that Bowtie 2 will not necessarily report the same
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diff changeset
1188 alignment for two identical reads. This is counter-intuitive for some users,
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diff changeset
1189 but might be more appropriate in situations where the input consists of many
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diff changeset
1190 identical reads.
0
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1191
15
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1192 -----
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1193
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1194
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diff changeset
1195 **Paired-end (and mate-pair) data in fastq format**
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1196
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diff changeset
1197 Paired end datasets can be represented as two individual datasets:
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1198
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1199 First dataset::
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1200
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1201 @1/1
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1202 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1203 +
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1204 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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1205 @2/1
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1206 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1207 +
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1208 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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1209
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1210 Second dataset::
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1211
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1212 @1/2
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1213 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1214 +
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1215 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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diff changeset
1216 @2/2
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diff changeset
1217 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1218 +
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1219 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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1220
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diff changeset
1221 Or a single *interleaved* dataset::
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1222
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1223 @1/1
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1224 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1225 +
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diff changeset
1226 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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diff changeset
1227 @1/2
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diff changeset
1228 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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diff changeset
1229 +
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diff changeset
1230 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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diff changeset
1231 @2/1
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diff changeset
1232 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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diff changeset
1233 +
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diff changeset
1234 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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diff changeset
1235 @2/2
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diff changeset
1236 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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diff changeset
1237 +
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diff changeset
1238 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1239 ]]></help>
2
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diff changeset
1240 <citations>
17
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1241 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1242 <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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1243 </citations>
0
96d2e31a3938 Imported from capsule None
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1244 </tool>